diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2e19564e8..f9de07e9e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,7 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.13
     hooks:
-      - id: black
\ No newline at end of file
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
diff --git a/example/ml/model.tar.gz b/example/ml/model.tar.gz
index e11a0f191..7d35e4493 100644
Binary files a/example/ml/model.tar.gz and b/example/ml/model.tar.gz differ
diff --git a/main.py b/main.py
deleted file mode 100644
index 94e3a8723..000000000
--- a/main.py
+++ /dev/null
@@ -1,16 +0,0 @@
-# This is a sample Python script.
-
-# Press ⌃R to execute it or replace it with your code.
-# Press Double ⇧ to search everywhere for classes, files, tool windows, actions, and settings.
-
-
-def print_hi(name):
-    # Use a breakpoint in the code line below to debug your script.
-    print(f'Hi, {name}')  # Press ⌘F8 to toggle the breakpoint.
-
-
-# Press the green button in the gutter to run the script.
-if __name__ == '__main__':
-    print_hi('PyCharm')
-
-# See PyCharm help at https://www.jetbrains.com/help/pycharm/
diff --git a/poetry.lock b/poetry.lock
index 7d11086d8..3c85de23d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -138,13 +138,13 @@ frozenlist = ">=1.1.0"
 
 [[package]]
 name = "alabaster"
-version = "0.7.12"
-description = "A configurable sidebar-enabled Sphinx theme"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
 optional = false
-python-versions = "*"
+python-versions = ">=3.9"
 files = [
-    {file = "alabaster-0.7.12-py2.py3-none-any.whl", hash = "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359"},
-    {file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
 [[package]]
@@ -185,55 +185,62 @@ idna = ">=2.5"
 
 [[package]]
 name = "arrow"
-version = "1.2.3"
+version = "1.3.0"
 description = "Better dates & times for Python"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
-    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+    {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
+    {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
 ]
 
 [package.dependencies]
 python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
 
 [[package]]
 name = "async-timeout"
-version = "4.0.2"
+version = "4.0.3"
 description = "Timeout context manager for asyncio programs"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "async-timeout-4.0.2.tar.gz", hash = "sha256:2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15"},
-    {file = "async_timeout-4.0.2-py3-none-any.whl", hash = "sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c"},
+    {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"},
+    {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"},
 ]
 
 [[package]]
 name = "attrs"
-version = "22.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7"
 files = [
-    {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
-    {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
 ]
 
 [package.extras]
-dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"]
-docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"]
-tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"]
-tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "autodocsumm"
-version = "0.2.11"
+version = "0.2.12"
 description = "Extended sphinx autodoc including automatic autosummaries"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "autodocsumm-0.2.11-py3-none-any.whl", hash = "sha256:f1d0a623bf1ad64d979a9e23fd360d1fb1b8f869beaf3197f711552cddc174e2"},
-    {file = "autodocsumm-0.2.11.tar.gz", hash = "sha256:183212bd9e9f3b58a96bb21b7958ee4e06224107aa45b2fd894b61b83581b9a9"},
+    {file = "autodocsumm-0.2.12-py3-none-any.whl", hash = "sha256:b842b53c686c07a4f174721ca4e729b027367703dbf42e2508863a3c6d6c049c"},
+    {file = "autodocsumm-0.2.12.tar.gz", hash = "sha256:848fe8c38df433c6635489499b969cb47cc389ed3d7b6e75c8ccbc94d4b3bf9e"},
 ]
 
 [package.dependencies]
@@ -241,67 +248,68 @@ Sphinx = ">=2.2,<8.0"
 
 [[package]]
 name = "babel"
-version = "2.11.0"
+version = "2.14.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.11.0-py3-none-any.whl", hash = "sha256:1ad3eca1c885218f6dce2ab67291178944f810a10a9b5f3cb8382a5a232b64fe"},
-    {file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"},
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
 ]
 
-[package.dependencies]
-pytz = ">=2015.7"
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.12.2"
+version = "4.12.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
-    {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
+    {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"},
+    {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
 ]
 
 [package.dependencies]
 soupsieve = ">1.2"
 
 [package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
 html5lib = ["html5lib"]
 lxml = ["lxml"]
 
 [[package]]
 name = "biopython"
-version = "1.81"
+version = "1.83"
 description = "Freely available tools for computational molecular biology."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "biopython-1.81-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ef7c79b65b0b3f3c7dc59e20a7f8ae5758d8e852cb8b9cace590dc5617e348ba"},
-    {file = "biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6ebfbce0d91796c7aef422ee9dffe8827e07e5abaa94545e006f1f20e965c80b"},
-    {file = "biopython-1.81-cp310-cp310-win32.whl", hash = "sha256:919a2c583cabf9c96d2ae4e1245a6b0376932fb342aca302a0fc198b71ab3275"},
-    {file = "biopython-1.81-cp310-cp310-win_amd64.whl", hash = "sha256:b37c0d24191e5c96ca02415a5188551980c83a0d518bbc4ffe3c9a5d1fe0ee81"},
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+    {file = "biopython-1.83-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:81d1e2515b380e1876720ba79dbf50f8ef3a38cc38ba5953ef61ec20d0934ee2"},
+    {file = "biopython-1.83-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ec82350c24cdcf34a8d4a5f189d0ff7dc025658098a60e6f0e681d24b6a1414e"},
+    {file = "biopython-1.83-cp39-cp39-win32.whl", hash = "sha256:e914f7161b3831d7c58db33cc5c7ca64b42c9877c5a776a8313e7a5fd494f8de"},
+    {file = "biopython-1.83-cp39-cp39-win_amd64.whl", hash = "sha256:aae1b156a76907c2abfe9d141776b0aead65695ea914eaecdf12bd1e8991f869"},
+    {file = "biopython-1.83.tar.gz", hash = "sha256:78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7"},
 ]
 
 [package.dependencies]
@@ -330,40 +338,125 @@ redis = ["redis (>=2.10.5)"]
 
 [[package]]
 name = "certifi"
-version = "2022.9.24"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
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-[package.extras]
-unicode-backport = ["unicodedata2"]
-
 [[package]]
 name = "click"
 version = "8.1.7"
@@ -448,32 +541,32 @@ tests = ["check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "mock
 
 [[package]]
 name = "distlib"
-version = "0.3.6"
+version = "0.3.8"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
 name = "dnspython"
-version = "2.2.1"
+version = "2.4.2"
 description = "DNS toolkit"
 optional = false
-python-versions = ">=3.6,<4.0"
+python-versions = ">=3.8,<4.0"
 files = [
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+dnssec = ["cryptography (>=2.6,<42.0)"]
+doh = ["h2 (>=4.1.0)", "httpcore (>=0.17.3)", "httpx (>=0.24.1)"]
+doq = ["aioquic (>=0.9.20)"]
 idna = ["idna (>=2.1,<4.0)"]
-trio = ["trio (>=0.14,<0.20)"]
+trio = ["trio (>=0.14,<0.23)"]
 wmi = ["wmi (>=1.5.1,<2.0.0)"]
 
 [[package]]
@@ -508,13 +601,13 @@ dates = ["pytz (>=2019.1)"]
 
 [[package]]
 name = "email-validator"
-version = "2.0.0.post2"
+version = "2.1.0.post1"
 description = "A robust email address syntax and deliverability validation library."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -542,13 +635,13 @@ sphinx = ["sphinx (>=3.4.0)", "sphinx-jinja2-compat (>=0.1.1)", "sphinx-toolbox
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.3"
+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -556,13 +649,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
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-version = "19.11.0"
+version = "22.2.0"
 description = "Faker is a Python package that generates fake data for you."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -570,150 +663,222 @@ python-dateutil = ">=2.4"
 
 [[package]]
 name = "filelock"
-version = "3.8.0"
+version = "3.13.1"
 description = "A platform independent file lock."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+typing = ["typing-extensions (>=4.8)"]
 
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+version = "1.4.1"
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 [[package]]
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 [[package]]
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-version = "2.5.9"
+version = "2.5.33"
 description = "File identification library for Python"
 optional = false
-python-versions = ">=3.7"
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 ]
 
 [package.extras]
@@ -753,13 +918,13 @@ license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
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 ]
 
 [[package]]
@@ -775,24 +940,24 @@ files = [
 
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-description = "iniconfig: brain-dead simple config-ini parsing"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
 optional = false
-python-versions = "*"
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 ]
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.3"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -818,85 +983,106 @@ tornado = {version = "*", markers = "python_version > \"2.7\""}
 
 [[package]]
 name = "markupsafe"
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+version = "2.1.3"
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 optional = false
 python-versions = ">=3.7"
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 ]
 
 [[package]]
 name = "motor"
-version = "3.2.0"
+version = "3.3.2"
 description = "Non-blocking MongoDB driver for Tornado or asyncio"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
-pymongo = ">=4.4,<5"
+pymongo = ">=4.5,<5"
 
 [package.extras]
-aws = ["pymongo[aws] (>=4.4,<5)"]
-encryption = ["pymongo[encryption] (>=4.4,<5)"]
-gssapi = ["pymongo[gssapi] (>=4.4,<5)"]
-ocsp = ["pymongo[ocsp] (>=4.4,<5)"]
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-srv = ["pymongo[srv] (>=4.4,<5)"]
-zstd = ["pymongo[zstd] (>=4.4,<5)"]
+aws = ["pymongo[aws] (>=4.5,<5)"]
+encryption = ["pymongo[encryption] (>=4.5,<5)"]
+gssapi = ["pymongo[gssapi] (>=4.5,<5)"]
+ocsp = ["pymongo[ocsp] (>=4.5,<5)"]
+snappy = ["pymongo[snappy] (>=4.5,<5)"]
+srv = ["pymongo[srv] (>=4.5,<5)"]
+test = ["aiohttp (<3.8.6)", "mockupdb", "motor[encryption]", "pytest (>=7)", "tornado (>=5)"]
+zstd = ["pymongo[zstd] (>=4.5,<5)"]
 
 [[package]]
 name = "motor-types"
-version = "1.0.0b3"
+version = "1.0.0b4"
 description = "Python stubs for Motor, a Non-Blocking MongoDB driver for Python's Tornado and AsyncIO based applications."
 optional = false
 python-versions = ">=3.8.0,<4.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -973,70 +1159,85 @@ files = [
 
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 ]
 
 [package.dependencies]
@@ -1415,35 +1622,22 @@ dnspython = ">=1.16.0,<3.0.0"
 
 [package.extras]
 aws = ["pymongo-auth-aws (<2.0.0)"]
-encryption = ["pymongo[aws]", "pymongocrypt (>=1.6.0,<2.0.0)"]
+encryption = ["certifi", "pymongo[aws]", "pymongocrypt (>=1.6.0,<2.0.0)"]
 gssapi = ["pykerberos", "winkerberos (>=0.5.0)"]
-ocsp = ["certifi", "pyopenssl (>=17.2.0)", "requests (<3.0.0)", "service-identity (>=18.1.0)"]
+ocsp = ["certifi", "cryptography (>=2.5)", "pyopenssl (>=17.2.0)", "requests (<3.0.0)", "service-identity (>=18.1.0)"]
 snappy = ["python-snappy"]
+test = ["pytest (>=7)"]
 zstd = ["zstandard"]
 
-[[package]]
-name = "pyparsing"
-version = "3.0.9"
-description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-optional = false
-python-versions = ">=3.6.8"
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-]
-
-[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
-
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1496,13 +1690,13 @@ testing = ["coverage (>=6.2)", "flaky (>=3.5.0)", "hypothesis (>=5.7.1)", "mypy
 
 [[package]]
 name = "pytest-mock"
-version = "3.10.0"
+version = "3.12.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1540,17 +1734,6 @@ files = [
 [package.dependencies]
 six = ">=1.5"
 
-[[package]]
-name = "pytz"
-version = "2022.6"
-description = "World timezone definitions, modern and historical"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [[package]]
 name = "pyyaml"
 version = "6.0.1"
@@ -1612,20 +1795,20 @@ files = [
 
 [[package]]
 name = "requests"
-version = "2.28.1"
+version = "2.31.0"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7, <4"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
-charset-normalizer = ">=2,<3"
+charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<1.27"
+urllib3 = ">=1.21.1,<3"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
@@ -1696,13 +1879,13 @@ files = [
 
 [[package]]
 name = "sentry-sdk"
-version = "1.32.0"
+version = "1.39.2"
 description = "Python client for Sentry (https://sentry.io)"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -1728,7 +1911,7 @@ huey = ["huey (>=2)"]
 loguru = ["loguru (>=0.5)"]
 opentelemetry = ["opentelemetry-distro (>=0.35b0)"]
 opentelemetry-experimental = ["opentelemetry-distro (>=0.40b0,<1.0)", "opentelemetry-instrumentation-aiohttp-client (>=0.40b0,<1.0)", "opentelemetry-instrumentation-django (>=0.40b0,<1.0)", "opentelemetry-instrumentation-fastapi (>=0.40b0,<1.0)", "opentelemetry-instrumentation-flask (>=0.40b0,<1.0)", "opentelemetry-instrumentation-requests (>=0.40b0,<1.0)", "opentelemetry-instrumentation-sqlite3 (>=0.40b0,<1.0)", "opentelemetry-instrumentation-urllib (>=0.40b0,<1.0)"]
-pure-eval = ["asttokens", "executing", "pure-eval"]
+pure-eval = ["asttokens", "executing", "pure_eval"]
 pymongo = ["pymongo (>=3.1)"]
 pyspark = ["pyspark (>=2.4.4)"]
 quart = ["blinker (>=1.1)", "quart (>=0.16.1)"]
@@ -1741,19 +1924,19 @@ tornado = ["tornado (>=5)"]
 
 [[package]]
 name = "setuptools"
-version = "65.6.3"
+version = "69.0.3"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "setuptools-69.0.3.tar.gz", hash = "sha256:be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78"},
 ]
 
 [package.extras]
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+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)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "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 (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -1957,47 +2140,50 @@ testing = ["coincidence (>=0.4.3)", "pygments (>=2.7.4,<=2.13.0)"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.2"
-description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
+version = "1.0.8"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-applehelp-1.0.2.tar.gz", hash = "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"},
-    {file = "sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a"},
+    {file = "sphinxcontrib_applehelp-1.0.8-py3-none-any.whl", hash = "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"},
+    {file = "sphinxcontrib_applehelp-1.0.8.tar.gz", hash = "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.2"
-description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+version = "1.0.6"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
-    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+    {file = "sphinxcontrib_devhelp-1.0.6-py3-none-any.whl", hash = "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f"},
+    {file = "sphinxcontrib_devhelp-1.0.6.tar.gz", hash = "sha256:9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.0"
+version = "2.0.5"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-htmlhelp-2.0.0.tar.gz", hash = "sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2"},
-    {file = "sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl", hash = "sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07"},
+    {file = "sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl", hash = "sha256:393f04f112b4d2f53d93448d4bce35842f62b307ccdc549ec1585e950bc35e04"},
+    {file = "sphinxcontrib_htmlhelp-2.0.5.tar.gz", hash = "sha256:0dc87637d5de53dd5eec3a6a01753b1ccf99494bd756aafecd74b4fa9e729015"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
 [[package]]
@@ -2016,48 +2202,50 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.3"
-description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
+version = "1.0.7"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
-    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+    {file = "sphinxcontrib_qthelp-1.0.7-py3-none-any.whl", hash = "sha256:e2ae3b5c492d58fcbd73281fbd27e34b8393ec34a073c792642cd8e529288182"},
+    {file = "sphinxcontrib_qthelp-1.0.7.tar.gz", hash = "sha256:053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.5"
-description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
+version = "1.1.10"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
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+    {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"},
+    {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"},
 ]
 
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "structlog"
-version = "23.2.0"
+version = "23.3.0"
 description = "Structured Logging for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "structlog-23.2.0-py3-none-any.whl", hash = "sha256:16a167e87b9fa7fae9a972d5d12805ef90e04857a93eba479d4be3801a6a1482"},
-    {file = "structlog-23.2.0.tar.gz", hash = "sha256:334666b94707f89dbc4c81a22a8ccd34449f0201d5b1ee097a030b577fa8c858"},
+    {file = "structlog-23.3.0-py3-none-any.whl", hash = "sha256:d6922a88ceabef5b13b9eda9c4043624924f60edbb00397f4d193bd754cde60a"},
+    {file = "structlog-23.3.0.tar.gz", hash = "sha256:24b42b914ac6bc4a4e6f716e82ac70d7fb1e8c3b1035a765591953bfc37101a5"},
 ]
 
 [package.extras]
 dev = ["structlog[tests,typing]"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-mermaid", "twisted"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-mermaid", "sphinxext-opengraph", "twisted"]
 tests = ["freezegun (>=0.2.8)", "pretend", "pytest (>=6.0)", "pytest-asyncio (>=0.17)", "simplejson"]
 typing = ["mypy (>=1.4)", "rich", "twisted"]
 
@@ -2103,50 +2291,61 @@ files = [
 
 [[package]]
 name = "tornado"
-version = "6.3.3"
+version = "6.4"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
 python-versions = ">= 3.8"
 files = [
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+    {file = "tornado-6.4-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:02ccefc7d8211e5a7f9e8bc3f9e5b0ad6262ba2fbb683a6443ecc804e5224ce0"},
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+    {file = "tornado-6.4-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f7894c581ecdcf91666a0912f18ce5e757213999e183ebfc2c3fdbf4d5bd764e"},
+    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e43bc2e5370a6a8e413e1e1cd0c91bedc5bd62a74a532371042a18ef19e10579"},
+    {file = "tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f0251554cdd50b4b44362f73ad5ba7126fc5b2c2895cc62b14a1c2d7ea32f212"},
+    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:fd03192e287fbd0899dd8f81c6fb9cbbc69194d2074b38f384cb6fa72b80e9c2"},
+    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_i686.whl", hash = "sha256:88b84956273fbd73420e6d4b8d5ccbe913c65d31351b4c004ae362eba06e1f78"},
+    {file = "tornado-6.4-cp38-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:71ddfc23a0e03ef2df1c1397d859868d158c8276a0603b96cf86892bff58149f"},
+    {file = "tornado-6.4-cp38-abi3-win32.whl", hash = "sha256:6f8a6c77900f5ae93d8b4ae1196472d0ccc2775cc1dfdc9e7727889145c45052"},
+    {file = "tornado-6.4-cp38-abi3-win_amd64.whl", hash = "sha256:10aeaa8006333433da48dec9fe417877f8bcc21f48dda8d661ae79da357b2a63"},
+    {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"},
+]
+
+[[package]]
+name = "types-python-dateutil"
+version = "2.8.19.20240106"
+description = "Typing stubs for python-dateutil"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "types-python-dateutil-2.8.19.20240106.tar.gz", hash = "sha256:1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f"},
+    {file = "types_python_dateutil-2.8.19.20240106-py3-none-any.whl", hash = "sha256:efbbdc54590d0f16152fa103c9879c7d4a00e82078f6e2cf01769042165acaa2"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.4.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.9.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.4.0-py3-none-any.whl", hash = "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e"},
-    {file = "typing_extensions-4.4.0.tar.gz", hash = "sha256:1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa"},
+    {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
+    {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "1.26.13"
+version = "2.1.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.8"
 files = [
-    {file = "urllib3-1.26.13-py2.py3-none-any.whl", hash = "sha256:47cc05d99aaa09c9e72ed5809b60e7ba354e64b59c9c173ac3018642d8bb41fc"},
-    {file = "urllib3-1.26.13.tar.gz", hash = "sha256:c083dd0dce68dbfbe1129d5271cb90f9447dea7d52097c6e0126120c521ddea8"},
+    {file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"},
+    {file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
-socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtool-core"
@@ -2173,23 +2372,23 @@ structlog = ">=23.1.0,<24.0.0"
 
 [[package]]
 name = "virtualenv"
-version = "20.17.0"
+version = "20.25.0"
 description = "Virtual Python Environment builder"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.17.0-py3-none-any.whl", hash = "sha256:40a7e06a98728fd5769e1af6fd1a706005b4bb7e16176a272ed4292473180389"},
-    {file = "virtualenv-20.17.0.tar.gz", hash = "sha256:7d6a8d55b2f73b617f684ee40fd85740f062e1f2e379412cb1879c7136f05902"},
+    {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"},
+    {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"},
 ]
 
 [package.dependencies]
-distlib = ">=0.3.6,<1"
-filelock = ">=3.4.1,<4"
-platformdirs = ">=2.4,<3"
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<5"
 
 [package.extras]
-docs = ["proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-argparse (>=0.3.2)", "sphinx-rtd-theme (>=1)", "towncrier (>=22.8)"]
-testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
 name = "webencodings"
@@ -2204,70 +2403,101 @@ files = [
 
 [[package]]
 name = "yarl"
-version = "1.8.1"
+version = "1.9.4"
 description = "Yet another URL library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "yarl-1.8.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:abc06b97407868ef38f3d172762f4069323de52f2b70d133d096a48d72215d28"},
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 ]
 
 [package.dependencies]
diff --git a/pyproject.toml b/pyproject.toml
index 98665c1d0..80dfa32df 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,17 +58,9 @@ exclude = [
     ".ruff_cache",
     "__pypackages__",
 ]
-indent-width = 4
-line-length = 88
-target-version = "py310"
 
 [tool.ruff.lint]
-fixable = ["ALL", "I001"]
-
-[tool.ruff.format]
-indent-style = "space"
-line-ending = "auto"
-quote-style = "double"
+select = ["ALL"]
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
diff --git a/tests/api/test_utils.py b/tests/api/test_utils.py
index f49055894..210201f8e 100644
--- a/tests/api/test_utils.py
+++ b/tests/api/test_utils.py
@@ -4,9 +4,7 @@
 
 
 async def test_retry(caplog):
-    """
-    Test that the retry utility retries failing HTTP requests and logs the attempts.
-    """
+    """Test that the retry utility retries failing HTTP requests and logs the attempts."""
     caplog.set_level(logging.INFO)
 
     class Retry:
diff --git a/tests/data/test_analyses.py b/tests/data/test_analyses.py
index 90ff00666..b0326fff9 100644
--- a/tests/data/test_analyses.py
+++ b/tests/data/test_analyses.py
@@ -3,14 +3,13 @@
 import pytest
 from pyfixtures import FixtureScope
 
-from virtool_workflow.pytest_plugin.data import Data
 from virtool_workflow.data.analyses import WFAnalysis
-from virtool_workflow.errors import JobsAPINotFound, JobsAPIConflict
+from virtool_workflow.errors import JobsAPIConflict, JobsAPINotFound
+from virtool_workflow.pytest_plugin.data import Data
 
 
 async def test_ok(data: Data, scope: FixtureScope):
-    """
-    Test that the analysis fixture returns an Analysis object with the expected values.
+    """Test that the analysis fixture returns an Analysis object with the expected values.
     """
     data.job.args["analysis_id"] = data.analysis.id
 
@@ -28,10 +27,9 @@ async def test_not_found(data: Data, scope: FixtureScope):
 
 
 async def test_upload_file(
-    captured_uploads_path: Path, data: Data, scope: FixtureScope, work_path: Path
+    captured_uploads_path: Path, data: Data, scope: FixtureScope, work_path: Path,
 ):
-    """
-    Test that the ``Analysis`` object returned by the fixture can be used to upload an
+    """Test that the ``Analysis`` object returned by the fixture can be used to upload an
     analysis file.
     """
     ...
@@ -42,7 +40,7 @@ async def test_upload_file(
 
     path = work_path / "blank.txt"
 
-    with open(path, "wt") as f:
+    with open(path, "w") as f:
         f.write("hello world")
 
     await analysis.upload_file(path, "unknown")
diff --git a/tests/data/test_ml.py b/tests/data/test_ml.py
index 16a8be73e..f853d1b61 100644
--- a/tests/data/test_ml.py
+++ b/tests/data/test_ml.py
@@ -2,11 +2,10 @@
 
 import pytest
 from pyfixtures import FixtureScope
-from syrupy import SnapshotAssertion
 from syrupy import SnapshotSession
 
-from virtool_workflow.pytest_plugin.data import Data
 from virtool_workflow.data.ml import WFMLModelRelease
+from virtool_workflow.pytest_plugin.data import Data
 
 test = SnapshotSession
 
@@ -21,11 +20,8 @@ async def test_ok(
         data: Data,
         example_path: Path,
         scope: FixtureScope,
-        snapshot: SnapshotAssertion,
-        work_path: Path,
     ):
-        """
-        Test that the ML fixture instantiates, contains the expected data, and
+        """Test that the ML fixture instantiates, contains the expected data, and
         downloads the sample files to the work path.
         """
         data.job.args["analysis_id"] = data.analysis.id
@@ -39,16 +35,20 @@ async def test_ok(
         assert ml.name == data.ml.name
 
         assert ml.path.is_dir()
-        assert (ml.path / "model.tar.gz").is_file()
-        assert ml.file_path == ml.path / "model.tar.gz"
-
-        assert (
-            open(ml.file_path, "rb").read()
-            == open(example_path / "ml/model.tar.gz", "rb").read()
-        )
+        assert sorted([p.name for p in ml.path.iterdir()]) == [
+            "mappability_profile.rds",
+            "model.tar.gz",
+            "nucleotide_info.csv",
+            "reference.json.gz",
+            "trained_rf.rds",
+            "trained_xgb.rds",
+            "virus_segments.rds",
+        ]
 
     async def test_none(
-        self, data: Data, scope: FixtureScope, snapshot: SnapshotAssertion
+        self,
+        data: Data,
+        scope: FixtureScope,
     ):
         """Test that the ML fixture returns None when no ML model is specified."""
         data.job.args["analysis_id"] = data.analysis.id
diff --git a/virtool_workflow/analysis/fastqc.py b/virtool_workflow/analysis/fastqc.py
index 85fcbe8e9..1e9e42b46 100644
--- a/virtool_workflow/analysis/fastqc.py
+++ b/virtool_workflow/analysis/fastqc.py
@@ -2,12 +2,12 @@
 from __future__ import annotations
 
 import asyncio
-import statistics
 import shutil
+import statistics
 import tempfile
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Protocol, TextIO, IO
+from typing import IO, Protocol, TextIO
 
 from pyfixtures import fixture
 
@@ -49,16 +49,16 @@ def composite(self, parser: BaseQualityParser):
                 mean=statistics.mean([this.mean, other.mean]),
                 median=statistics.mean([this.median, other.median]),
                 lower_quartile=statistics.mean(
-                    [this.lower_quartile, other.lower_quartile]
+                    [this.lower_quartile, other.lower_quartile],
                 ),
                 upper_quartile=statistics.mean(
-                    [this.upper_quartile, other.upper_quartile]
+                    [this.upper_quartile, other.upper_quartile],
                 ),
                 tenth_percentile=statistics.mean(
-                    [this.tenth_percentile, other.tenth_percentile]
+                    [this.tenth_percentile, other.tenth_percentile],
                 ),
                 ninetieth_percentile=statistics.mean(
-                    [this.ninetieth_percentile, other.ninetieth_percentile]
+                    [this.ninetieth_percentile, other.ninetieth_percentile],
                 ),
             )
             for this, other in zip(self.data, parser.data)
@@ -109,7 +109,7 @@ def handle(self, f: TextIO):
                         upper_quartile=upper_quartile,
                         tenth_percentile=tenth_percentile,
                         ninetieth_percentile=ninetieth_percentile,
-                    )
+                    ),
                 )
 
                 if i - max_index != 1:
@@ -208,7 +208,7 @@ def handle(self, f: TextIO):
             split = line.split()
 
             try:
-                g, a, t, c = [float(value) for value in split[1:]]
+                g, a, t, c = (float(value) for value in split[1:])
             except ValueError as err:
                 if "NaN" not in str(err):
                     raise
@@ -276,8 +276,7 @@ def _calculate_index_range(base: str) -> range:
 
 
 def _handle_base_quality_nan(split_line: list) -> list:
-    """
-    Parse a per-base quality line from FastQC containing NaN values.
+    """Parse a per-base quality line from FastQC containing NaN values.
 
     :param split_line: the quality line split into a :class:`.List`
     :return: replacement values
@@ -301,8 +300,7 @@ def _handle_base_quality_nan(split_line: list) -> list:
 
 
 def _parse_fastqc(fastqc_path: Path, output_path: Path) -> dict:
-    """
-    Parse the FastQC results at `fastqc_path`.
+    """Parse the FastQC results at `fastqc_path`.
 
     All FastQC data except the textual data file are removed.
 
@@ -333,7 +331,7 @@ def _parse_fastqc(fastqc_path: Path, output_path: Path) -> dict:
             nucleotide_composition = NucleotideCompositionParser()
             sequence_quality = SequenceQualityParser()
 
-            with open(new_path, "r") as f:
+            with open(new_path) as f:
                 while True:
                     line = f.readline()
 
@@ -358,7 +356,7 @@ def _parse_fastqc(fastqc_path: Path, output_path: Path) -> dict:
                     basic_statistics=basic_statistics,
                     nucleotide_composition=nucleotide_composition,
                     sequence_quality=sequence_quality,
-                )
+                ),
             )
 
     if len(sides) == 1:
@@ -412,7 +410,7 @@ def _parse_fastqc(fastqc_path: Path, output_path: Path) -> dict:
         "composition": [
             [round(n, 1) for n in [point.g, point.a, point.t, point.c]]
             for point in left.nucleotide_composition.composite(
-                right.nucleotide_composition
+                right.nucleotide_composition,
             ).data
         ],
         "count": basic.count,
@@ -432,14 +430,13 @@ async def __call__(self, paths: ReadPaths, output_path: Path) -> dict:
 
 @fixture
 async def fastqc(run_subprocess: RunSubprocess):
-    """
-    Provides an asynchronous function that can run FastQC as a subprocess.
+    """Provides an asynchronous function that can run FastQC as a subprocess.
 
     The function takes a one or two paths to FASTQ read files (:class:`.ReadPaths`) in
     a tuple.
 
     Example:
-
+    -------
     .. code-block:: python
 
         @step
diff --git a/virtool_workflow/analysis/skewer.py b/virtool_workflow/analysis/skewer.py
index a8c803439..80c1f827a 100644
--- a/virtool_workflow/analysis/skewer.py
+++ b/virtool_workflow/analysis/skewer.py
@@ -1,5 +1,5 @@
-"""
-Utilities and a fixture for using `Skewer <https://github.com/relipmoc/skewer>`_ to trim reads.
+"""Utilities and a fixture for using `Skewer <https://github.com/relipmoc/skewer>`_ to
+trim reads.
 """
 import asyncio
 import os
@@ -85,18 +85,16 @@ class SkewerResult:
 
     @property
     def left(self) -> Path:
-        """
-        The path to one of:
-            - the FASTQ trimming result for an unpaired Illumina dataset
-            - the FASTA trimming result for the left reads of a paired Illumina dataset
+        """The path to one of:
+        - the FASTQ trimming result for an unpaired Illumina dataset
+        - the FASTA trimming result for the left reads of a paired Illumina dataset
 
         """
         return self.read_paths[0]
 
     @property
     def right(self) -> Path | None:
-        """
-        The path to the rights reads of a paired Illumina dataset.
+        """The path to the rights reads of a paired Illumina dataset.
 
         ``None`` if the dataset in unpaired.
 
@@ -110,16 +108,14 @@ def right(self) -> Path | None:
 
 
 def calculate_skewer_trimming_parameters(
-    sample: WFSample, min_read_length: int
+    sample: WFSample, min_read_length: int,
 ) -> SkewerConfiguration:
-    """
-    Calculates trimming parameters based on the library type, and minimum allowed trim length.
+    """Calculates trimming parameters based on the library type, and minimum allowed trim length.
 
     :param sample: The sample to calculate trimming parameters for.
     :param min_read_length: The minimum length of a read before it is discarded.
     :return: the trimming parameters
     """
-
     config = SkewerConfiguration(
         min_length=min_read_length,
         mode=SkewerMode.PAIRED_END if sample.paired else SkewerMode.SINGLE_END,
@@ -145,15 +141,14 @@ class SkewerRunner(Protocol):
     """A protocol describing callables that can be used to run Skewer."""
 
     async def __call__(
-        self, config: SkewerConfiguration, paths: ReadPaths, output_path: Path
+        self, config: SkewerConfiguration, paths: ReadPaths, output_path: Path,
     ) -> SkewerResult:
         ...
 
 
 @fixture
 def skewer(proc: int, run_subprocess: RunSubprocess) -> SkewerRunner:
-    """
-    Provides an asynchronous function that can run skewer.
+    """Provides an asynchronous function that can run skewer.
 
     The provided function takes a :class:`.SkewerConfiguration` and a tuple of paths to
     the left and right reads to trim. If a single member tuple is provided, the dataset
@@ -163,7 +158,7 @@ def skewer(proc: int, run_subprocess: RunSubprocess) -> SkewerRunner:
     for the workflow run.
 
     Example:
-
+    -------
     .. code-block:: python
 
         @step
@@ -183,7 +178,7 @@ async def step_one(skewer: SkewerRunner, work_path: Path):
         raise RuntimeError("skewer is not installed.")
 
     async def func(
-        config: SkewerConfiguration, read_paths: ReadPaths, output_path: Path
+        config: SkewerConfiguration, read_paths: ReadPaths, output_path: Path,
     ):
         temp_path = Path(await asyncio.to_thread(mkdtemp, suffix="_virtool_skewer"))
 
@@ -224,7 +219,7 @@ async def func(
         )
 
         read_paths = await asyncio.to_thread(
-            _rename_trimming_results, temp_path, output_path
+            _rename_trimming_results, temp_path, output_path,
         )
 
         return SkewerResult(command, output_path, process, read_paths)
@@ -233,12 +228,10 @@ async def func(
 
 
 def _rename_trimming_results(temp_path: Path, output_path: Path) -> ReadPaths:
-    """
-    Rename Skewer output to a simple name used in Virtool.
+    """Rename Skewer output to a simple name used in Virtool.
 
     :param path: The path containing the results from Skewer
     """
-
     shutil.move(
         temp_path / "reads-trimmed.log",
         output_path / "trim.log",
diff --git a/virtool_workflow/analysis/trimming.py b/virtool_workflow/analysis/trimming.py
index 93f3971b7..8511d87e2 100644
--- a/virtool_workflow/analysis/trimming.py
+++ b/virtool_workflow/analysis/trimming.py
@@ -8,10 +8,9 @@
 
 
 def calculate_trimming_cache_key(
-    sample_id: str, trimming_parameters: dict, program: str = "skewer"
+    sample_id: str, trimming_parameters: dict, program: str = "skewer",
 ):
-    """
-    Compute a unique cache key.
+    """Compute a unique cache key.
 
     **This is not currently used.**
 
@@ -21,7 +20,6 @@ def calculate_trimming_cache_key(
     :return: A unique cache key.
 
     """
-
     raw_key = "reads-" + json.dumps(
         {
             "id": sample_id,
@@ -35,8 +33,7 @@ def calculate_trimming_cache_key(
 
 
 def calculate_trimming_min_length(sample: WFSample) -> int:
-    """
-    Calculate the minimum trimming length that should be used for the passed sample.
+    """Calculate the minimum trimming length that should be used for the passed sample.
 
     This takes into account the library type (:class:`.LibraryType`) and the maximum
     observed read length in the sample.
diff --git a/virtool_workflow/api/acquire.py b/virtool_workflow/api/acquire.py
index 4b05f1e3b..5d3d1592a 100644
--- a/virtool_workflow/api/acquire.py
+++ b/virtool_workflow/api/acquire.py
@@ -1,10 +1,10 @@
 import asyncio
 
-from aiohttp import ClientSession, TCPConnector, ClientConnectionError
+from aiohttp import ClientConnectionError, ClientSession, TCPConnector
 from structlog import get_logger
 from virtool_core.models.job import JobAcquired
 
-from virtool_workflow.errors import JobAlreadyAcquired, JobsAPIServerError, JobsAPIError
+from virtool_workflow.errors import JobAlreadyAcquired, JobsAPIError, JobsAPIServerError
 
 logger = get_logger("api")
 
@@ -13,16 +13,14 @@ async def acquire_job_by_id(
     jobs_api_connection_string: str,
     job_id: str,
 ) -> JobAcquired:
-    """
-    Acquire the job with a given ID via the API.
+    """Acquire the job with a given ID via the API.
 
     :param jobs_api_connection_string: The url for the jobs API.
     :param job_id: The id of the job to acquire
     :return: a job including its API key
     """
-
     async with ClientSession(
-        connector=TCPConnector(force_close=True, limit=100)
+        connector=TCPConnector(force_close=True, limit=100),
     ) as session:
         attempts = 4
 
diff --git a/virtool_workflow/api/client.py b/virtool_workflow/api/client.py
index e4fcac6f5..cfdbd65a2 100644
--- a/virtool_workflow/api/client.py
+++ b/virtool_workflow/api/client.py
@@ -2,14 +2,14 @@
 from pathlib import Path
 
 import aiofiles
-from aiohttp import ClientSession, BasicAuth
+from aiohttp import BasicAuth, ClientSession
 
 from virtool_workflow.api.utils import (
-    raise_exception_by_status_code,
     decode_json_response,
+    raise_exception_by_status_code,
 )
-from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.errors import JobsAPIError
+from virtool_workflow.files import VirtoolFileFormat
 
 CHUNK_SIZE = 1024 * 1024 * 2
 
@@ -21,19 +21,17 @@ def __init__(self, http: ClientSession, jobs_api_connection_string: str):
 
     async def get_json(self, path: str) -> dict:
         """Get the JSON response from the provided API ``path``."""
-
         async with self.http.get(f"{self.jobs_api_connection_string}{path}") as resp:
             await raise_exception_by_status_code(resp)
             return await decode_json_response(resp)
 
     async def get_file(self, path: str, target_path: Path):
-        """
-        Download the file at URL ``path`` to the local filesystem path ``target_path``.
+        """Download the file at URL ``path`` to the local filesystem path ``target_path``.
         """
         async with self.http.get(f"{self.jobs_api_connection_string}{path}") as resp:
             if resp.status != 200:
                 raise JobsAPIError(
-                    f"Encountered {resp.status} while downloading '{path}'"
+                    f"Encountered {resp.status} while downloading '{path}'",
                 )
             async with aiofiles.open(target_path, "wb") as f:
                 async for chunk in resp.content.iter_chunked(CHUNK_SIZE):
@@ -42,8 +40,7 @@ async def get_file(self, path: str, target_path: Path):
             return target_path
 
     async def patch_json(self, path: str, data: dict) -> dict:
-        """
-        Make a patch request against the provided API ``path`` and return the response
+        """Make a patch request against the provided API ``path`` and return the response
         as a dictionary of decoded JSON.
 
         :param path: the API path to make the request against
@@ -51,7 +48,7 @@ async def patch_json(self, path: str, data: dict) -> dict:
         :return: the response as a dictionary of decoded JSON
         """
         async with self.http.patch(
-            f"{self.jobs_api_connection_string}{path}", json=data
+            f"{self.jobs_api_connection_string}{path}", json=data,
         ) as resp:
             await raise_exception_by_status_code(resp)
             return await decode_json_response(resp)
@@ -78,7 +75,7 @@ async def post_file(
 
     async def post_json(self, path: str, data: dict) -> dict:
         async with self.http.post(
-            f"{self.jobs_api_connection_string}{path}", json=data
+            f"{self.jobs_api_connection_string}{path}", json=data,
         ) as resp:
             await raise_exception_by_status_code(resp)
             return await decode_json_response(resp)
@@ -105,7 +102,7 @@ async def put_file(
 
     async def put_json(self, path: str, data: dict) -> dict:
         async with self.http.put(
-            f"{self.jobs_api_connection_string}{path}", json=data
+            f"{self.jobs_api_connection_string}{path}", json=data,
         ) as resp:
             await raise_exception_by_status_code(resp)
             return await decode_json_response(resp)
@@ -127,10 +124,9 @@ async def api_client(
     job_id: str,
     key: str,
 ):
-    """
-    An authenticated :class:``APIClient`` to make requests against the jobs API.
+    """An authenticated :class:``APIClient`` to make requests against the jobs API.
     """
     async with ClientSession(
-        auth=BasicAuth(login=f"job-{job_id}", password=key)
+        auth=BasicAuth(login=f"job-{job_id}", password=key),
     ) as http:
         yield APIClient(http, jobs_api_connection_string)
diff --git a/virtool_workflow/api/utils.py b/virtool_workflow/api/utils.py
index cb4da98e4..878be0f3c 100644
--- a/virtool_workflow/api/utils.py
+++ b/virtool_workflow/api/utils.py
@@ -2,27 +2,26 @@
 import functools
 
 from aiohttp import (
-    ServerDisconnectedError,
     ClientConnectorError,
     ClientResponse,
     ContentTypeError,
+    ServerDisconnectedError,
 )
 from structlog import get_logger
 
 from virtool_workflow.errors import (
-    JobsAPIServerError,
-    JobsAPINotFound,
     JobsAPIBadRequest,
-    JobsAPIForbidden,
     JobsAPIConflict,
+    JobsAPIForbidden,
+    JobsAPINotFound,
+    JobsAPIServerError,
 )
 
 logger = get_logger("api")
 
 
 def retry(func):
-    """
-    Retry an API call five times when encountering the following exceptions:
+    """Retry an API call five times when encountering the following exceptions:
       * ``ConnectionRefusedError``.
       * ``ClientConnectorError``.
       * ``ServerDisconnectedError``.
@@ -47,7 +46,7 @@ async def wrapped(*args, **kwargs):
 
             attempts += 1
             get_logger("runtime").info(
-                f"Encountered {type(err).__name__}. Retrying in 5 seconds."
+                f"Encountered {type(err).__name__}. Retrying in 5 seconds.",
             )
             await asyncio.sleep(5)
 
@@ -57,8 +56,7 @@ async def wrapped(*args, **kwargs):
 
 
 async def decode_json_response(resp: ClientResponse) -> dict | list | None:
-    """
-    Decode a JSON response from a :class:``ClientResponse``.
+    """Decode a JSON response from a :class:``ClientResponse``.
 
     Raise a :class:`ValueError` if the response is not JSON.
 
@@ -72,8 +70,7 @@ async def decode_json_response(resp: ClientResponse) -> dict | list | None:
 
 
 async def raise_exception_by_status_code(resp: ClientResponse):
-    """
-    Raise an exception based on the status code of the response.
+    """Raise an exception based on the status code of the response.
 
     :param resp: the response to check
     :raise JobsAPIBadRequest: the response status code is 400
@@ -108,5 +105,5 @@ async def raise_exception_by_status_code(resp: ClientResponse):
             raise status_exception_map[resp.status](message)
         else:
             raise ValueError(
-                f"Status code {resp.status} not handled for response\n {resp}"
+                f"Status code {resp.status} not handled for response\n {resp}",
             )
diff --git a/virtool_workflow/data/analyses.py b/virtool_workflow/data/analyses.py
index 823ddc9d6..e36eb6694 100644
--- a/virtool_workflow/data/analyses.py
+++ b/virtool_workflow/data/analyses.py
@@ -52,17 +52,14 @@ def __init__(
         """The workflow being run to populate the analysis."""
 
     async def delete(self):
-        """
-        Delete the analysis.
+        """Delete the analysis.
 
         This method should be called if the workflow fails before a result is uploaded.
         """
-
         await self._api.delete(f"/analyses/{self.id}")
 
     async def upload_file(self, path: Path, fmt: VirtoolFileFormat = "unknown"):
-        """
-        Upload files in the workflow environment that should be associated with the
+        """Upload files in the workflow environment that should be associated with the
         current analysis.
 
         :param path: the path to the file to upload
@@ -76,8 +73,7 @@ async def upload_file(self, path: Path, fmt: VirtoolFileFormat = "unknown"):
         )
 
     async def upload_result(self, results: dict[str, Any]):
-        """
-        Upload the results dict for the analysis.
+        """Upload the results dict for the analysis.
 
         :param results: the analysis results
         """
@@ -89,8 +85,7 @@ async def analysis(
     _api: APIClient,
     job: Job,
 ) -> WFAnalysis:
-    """
-    A :class:`.WFAnalysis` object that represents the analysis associated with the running
+    """A :class:`.WFAnalysis` object that represents the analysis associated with the running
     workflow.
     """
     id_ = job.args["analysis_id"]
diff --git a/virtool_workflow/data/hmms.py b/virtool_workflow/data/hmms.py
index 7e2d1fba7..5fb55ef5f 100644
--- a/virtool_workflow/data/hmms.py
+++ b/virtool_workflow/data/hmms.py
@@ -17,8 +17,7 @@
 
 @dataclass
 class WFHMMs:
-    """
-    A class that exposes:
+    """A class that exposes:
 
     1. A :class:`dict` the links `HMMER <http://hmmer.org/>`_ cluster IDs to Virtool
        annotation IDs.
@@ -37,24 +36,21 @@ class WFHMMs:
 
     @cached_property
     def cluster_annotation_map(self) -> dict[int, str]:
-        """
-        A :class:`dict` that maps cluster IDs used to identify HMMs in
+        """A :class:`dict` that maps cluster IDs used to identify HMMs in
         `HMMER <http://hmmer.org/>`_ to annotation IDs used in Virtool.
         """
         return {hmm.cluster: hmm.id for hmm in self.annotations}
 
     @property
     def profiles_path(self):
-        """
-        The path to the ``profiles.hmm`` file.
+        """The path to the ``profiles.hmm`` file.
 
         It can be provided directly to HMMER.
         """
         return self.path / "profiles.hmm"
 
     def get_id_by_cluster(self, cluster: int) -> str:
-        """
-        Get the Virtool HMM annotation ID for a given cluster ID.
+        """Get the Virtool HMM annotation ID for a given cluster ID.
 
         :param cluster: a cluster ID
         :return: the corresponding annotation ID
@@ -69,8 +65,7 @@ async def hmms(
     run_subprocess: RunSubprocess,
     work_path: Path,
 ):
-    """
-    A fixture for accessing HMM data.
+    """A fixture for accessing HMM data.
 
     The ``*.hmm`` file is copied from the data directory and ``hmmpress`` is run to
     create all the HMM files.
diff --git a/virtool_workflow/data/indexes.py b/virtool_workflow/data/indexes.py
index 0cdc13719..034413dc9 100644
--- a/virtool_workflow/data/indexes.py
+++ b/virtool_workflow/data/indexes.py
@@ -13,8 +13,8 @@
 from virtool_core.utils import decompress_file
 
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.errors import MissingJobArgument
+from virtool_workflow.files import VirtoolFileFormat
 
 logger = get_logger("api")
 
@@ -43,16 +43,14 @@ class WFIndex:
 
     @property
     def bowtie_path(self) -> Path:
-        """
-        The path to the Bowtie2 index prefix for the Virtool index.
+        """The path to the Bowtie2 index prefix for the Virtool index.
 
         """
         return self.path / "reference"
 
     @property
     def fasta_path(self) -> Path:
-        """
-        The path to the complete FASTA file for the reference index in the workflow's
+        """The path to the complete FASTA file for the reference index in the workflow's
         work directory.
 
         """
@@ -60,16 +58,14 @@ def fasta_path(self) -> Path:
 
     @property
     def json_path(self) -> Path:
-        """
-        The path to the JSON representation of the reference index in the workflow's
+        """The path to the JSON representation of the reference index in the workflow's
         work directory.
 
         """
         return self.path / "otus.json"
 
     def get_otu_id_by_sequence_id(self, sequence_id: str) -> str:
-        """
-        Get the ID of the parent OTU for the given ``sequence_id``.
+        """Get the ID of the parent OTU for the given ``sequence_id``.
 
         :param sequence_id: the sequence ID
         :return: the matching OTU ID
@@ -81,8 +77,7 @@ def get_otu_id_by_sequence_id(self, sequence_id: str) -> str:
             raise ValueError("The sequence_id does not exist in the index")
 
     def get_sequence_length(self, sequence_id: str) -> int:
-        """
-        Get the sequence length for the given ``sequence_id``.
+        """Get the sequence length for the given ``sequence_id``.
 
         :param sequence_id: the sequence ID
         :return: the length of the sequence
@@ -98,8 +93,7 @@ async def write_isolate_fasta(
         otu_ids: list[str],
         path: Path,
     ) -> dict[str, int]:
-        """
-        Generate a FASTA file for all the isolates of the OTUs specified by ``otu_ids``.
+        """Generate a FASTA file for all the isolates of the OTUs specified by ``otu_ids``.
 
         :param otu_ids: the list of OTU IDs for which to generate and index
         :param path: the path to the reference index directory
@@ -157,10 +151,9 @@ async def finalize(self):
         await self._api.patch_json(f"/indexes/{self.id}", {})
 
     async def upload(
-        self, path: Path, fmt: VirtoolFileFormat = "fasta", name: str | None = None
+        self, path: Path, fmt: VirtoolFileFormat = "fasta", name: str | None = None,
     ):
-        """
-        Upload a file to associate with the index being built.
+        """Upload a file to associate with the index being built.
 
         Allowed file names are:
 
@@ -186,8 +179,7 @@ async def upload(
 
     @property
     def otus_json_path(self) -> Path:
-        """
-        The path to the JSON representation of the reference index in the workflow's
+        """The path to the JSON representation of the reference index in the workflow's
         work directory.
 
         """
@@ -280,10 +272,9 @@ async def index(
 
 @fixture
 async def new_index(
-    _api: APIClient, job: Job, proc: int, work_path: Path
+    _api: APIClient, job: Job, proc: int, work_path: Path,
 ) -> WFNewIndex:
-    """
-    The :class:`.WFNewIndex` for an index being created by the current job.
+    """The :class:`.WFNewIndex` for an index being created by the current job.
     """
     try:
         id_ = job.args["index_id"]
diff --git a/virtool_workflow/data/jobs.py b/virtool_workflow/data/jobs.py
index 9dd5e1ede..d49029771 100644
--- a/virtool_workflow/data/jobs.py
+++ b/virtool_workflow/data/jobs.py
@@ -2,9 +2,9 @@
 
 from pyfixtures import fixture
 from structlog import get_logger
-from virtool_core.models.job import JobState, JobAcquired, Job
+from virtool_core.models.job import Job, JobAcquired, JobState
 
-from virtool_workflow import WorkflowStep, Workflow
+from virtool_workflow import Workflow, WorkflowStep
 from virtool_workflow.api.client import APIClient
 
 MAX_TB = 50
diff --git a/virtool_workflow/data/ml.py b/virtool_workflow/data/ml.py
index 112ba67b3..4cc4d3503 100644
--- a/virtool_workflow/data/ml.py
+++ b/virtool_workflow/data/ml.py
@@ -1,4 +1,6 @@
 """A fixture and dataclass for working with machine learning models in workflows."""
+import asyncio
+import shutil
 from dataclasses import dataclass
 from pathlib import Path
 
@@ -8,15 +10,14 @@
 
 from virtool_workflow.api.client import APIClient
 from virtool_workflow.data.analyses import WFAnalysis
-from virtool_workflow.utils import make_directory
+from virtool_workflow.utils import make_directory, move_all_model_files, untar
 
 logger = get_logger("api")
 
 
 @dataclass
 class WFMLModelRelease:
-    """
-    A machine learning model.
+    """A machine learning model.
 
     This class represents a machine learning model and the selected release of that
     model in the workflow.
@@ -39,7 +40,9 @@ def file_path(self) -> Path:
 
 @fixture
 async def ml(
-    _api: APIClient, analysis: WFAnalysis, work_path: Path
+    _api: APIClient,
+    analysis: WFAnalysis,
+    work_path: Path,
 ) -> WFMLModelRelease | None:
     if analysis.ml is None:
         return None
@@ -50,11 +53,11 @@ async def ml(
     log = logger.bind(model_id=analysis.ml.id, model_release_id=model_release_id)
 
     model_release_json = await _api.get_json(
-        f"/ml/{model_id}/releases/{model_release_id}"
+        f"/ml/{model_id}/releases/{model_release_id}",
     )
     model_release = MLModelRelease(**model_release_json)
 
-    log.info("Fetched ML model release json")
+    log.info("fetched ml model release json")
 
     release = WFMLModelRelease(
         id=model_release.id,
@@ -65,9 +68,14 @@ async def ml(
     await make_directory(release.path)
 
     await _api.get_file(
-        f"/ml/{model_id}/releases/{model_release_id}/model.tar.gz", release.file_path
+        f"/ml/{model_id}/releases/{model_release_id}/model.tar.gz",
+        release.file_path,
     )
 
-    log.info("Downloaded ML model data file")
+    await asyncio.to_thread(untar, release.file_path, release.path)
+    await asyncio.to_thread(move_all_model_files, release.path / "model", release.path)
+    await asyncio.to_thread(shutil.rmtree, release.path / "model")
+
+    log.info("downloaded ml model release file")
 
     return release
diff --git a/virtool_workflow/data/samples.py b/virtool_workflow/data/samples.py
index 9e9bac94a..bbe2f6e8c 100644
--- a/virtool_workflow/data/samples.py
+++ b/virtool_workflow/data/samples.py
@@ -7,13 +7,13 @@
 from structlog import get_logger
 from virtool_core.models.enums import LibraryType
 from virtool_core.models.job import Job
-from virtool_core.models.samples import Sample, Quality
+from virtool_core.models.samples import Quality, Sample
 
 from virtool_workflow.analysis.utils import ReadPaths
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.data.uploads import WFUploads
 from virtool_workflow.errors import JobsAPINotFound
+from virtool_workflow.files import VirtoolFileFormat
 
 logger = get_logger("api")
 
@@ -42,8 +42,7 @@ class WFSample:
 
     @property
     def min_length(self) -> int | None:
-        """
-        The minimum observed read length in the sample sequencing data.
+        """The minimum observed read length in the sample sequencing data.
 
         Returns ``None`` if the sample is still being created and no quality data is available.
 
@@ -52,8 +51,7 @@ def min_length(self) -> int | None:
 
     @property
     def max_length(self) -> int | None:
-        """
-        The maximum observed read length in the sample sequencing data.
+        """The maximum observed read length in the sample sequencing data.
 
         Returns ``None`` if the sample is still being created and no quality data is available.
 
@@ -85,10 +83,9 @@ class WFNewSample:
 
 @fixture
 async def sample(
-    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path
+    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path,
 ) -> WFSample:
     """The sample associated with the current job."""
-
     id_ = job.args["sample_id"]
 
     base_url_path = f"/samples/{id_}"
@@ -104,7 +101,7 @@ async def sample(
     await asyncio.to_thread(reads_path.mkdir, exist_ok=True, parents=True)
 
     await _api.get_file(
-        f"{base_url_path}/reads/reads_1.fq.gz", reads_path / "reads_1.fq.gz"
+        f"{base_url_path}/reads/reads_1.fq.gz", reads_path / "reads_1.fq.gz",
     )
 
     if sample.paired:
@@ -113,7 +110,7 @@ async def sample(
             reads_path / "reads_2.fq.gz",
         )
         await _api.get_file(
-            f"{base_url_path}/reads/reads_2.fq.gz", reads_path / "reads_2.fq.gz"
+            f"{base_url_path}/reads/reads_2.fq.gz", reads_path / "reads_2.fq.gz",
         )
     else:
         read_paths = (reads_path / "reads_1.fq.gz",)
@@ -130,10 +127,9 @@ async def sample(
 
 @fixture
 async def new_sample(
-    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path
+    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path,
 ) -> WFNewSample:
     """The sample associated with the current job."""
-
     id_ = job.args["sample_id"]
 
     log = logger.bind(resource="sample", id=id_)
diff --git a/virtool_workflow/data/subtractions.py b/virtool_workflow/data/subtractions.py
index 17b4f33b2..28fef9050 100644
--- a/virtool_workflow/data/subtractions.py
+++ b/virtool_workflow/data/subtractions.py
@@ -7,8 +7,8 @@
 from structlog import get_logger
 from virtool_core.models.job import Job
 from virtool_core.models.subtraction import (
-    Subtraction,
     NucleotideComposition,
+    Subtraction,
     SubtractionFile,
 )
 
@@ -22,8 +22,7 @@
 
 @dataclass
 class WFSubtraction:
-    """
-    A Virtool subtraction that has been loaded into the workflow environment.
+    """A Virtool subtraction that has been loaded into the workflow environment.
 
     The subtraction files are downloaded to the workflow's local work path so they can
     be used for analysis.
@@ -47,7 +46,7 @@ class WFSubtraction:
     path: Path
     """
     The path to the subtraction directory.
- 
+
     The subtraction directory contains the FASTA and Bowtie2 files for the subtraction.
     """
 
@@ -58,8 +57,7 @@ def fasta_path(self) -> Path:
 
     @property
     def bowtie2_index_path(self) -> Path:
-        """
-        The path to Bowtie2 prefix in the running workflow's work_path
+        """The path to Bowtie2 prefix in the running workflow's work_path
 
         For example, ``/work/subtractions/<id>/subtraction`` refers to the Bowtie2
         index that comprises the files:
@@ -85,7 +83,7 @@ class WFNewSubtraction:
     A callable that deletes the subtraction from Virtool.
 
     This should be called if the subtraction creation fails before the subtraction is
-    finalized.    
+    finalized.
     """
 
     finalize: Callable[[dict[str, int | float], int], Coroutine[None, None, None]]
@@ -120,10 +118,9 @@ def fasta_path(self) -> Path:
 
 @fixture
 async def subtractions(
-    _api: APIClient, analysis: WFAnalysis, work_path: Path
+    _api: APIClient, analysis: WFAnalysis, work_path: Path,
 ) -> list[WFSubtraction]:
     """The subtractions to be used for the current analysis job."""
-
     subtraction_work_path = work_path / "subtractions"
     await asyncio.to_thread(subtraction_work_path.mkdir)
 
@@ -161,10 +158,9 @@ async def subtractions(
 
 @fixture
 async def new_subtraction(
-    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path
+    _api: APIClient, job: Job, uploads: WFUploads, work_path: Path,
 ) -> WFNewSubtraction:
-    """
-    A new subtraction that will be created during the current job.
+    """A new subtraction that will be created during the current job.
 
     Currently only used for the `create-subtraction` workflow.
     """
@@ -193,8 +189,7 @@ async def delete():
         await _api.delete(f"/subtractions/{subtraction_.id}")
 
     async def finalize(gc: dict[str, int | float], count: int):
-        """
-        Finalize the subtraction by setting the gc.
+        """Finalize the subtraction by setting the gc.
 
         :param gc: the nucleotide composition of the subtraction
         :param count: the number of sequences in the FASTA file
@@ -205,8 +200,7 @@ async def finalize(gc: dict[str, int | float], count: int):
         await _api.patch_json(url_path, {"gc": gc_.dict(), "count": count})
 
     async def upload(path: Path):
-        """
-        Upload a file relating to this subtraction.
+        """Upload a file relating to this subtraction.
 
         Filenames must be one of:
             - subtraction.fa.gz
@@ -227,7 +221,7 @@ async def upload(path: Path):
         log.info("Uploading subtraction file")
 
         await _api.put_file(
-            f"/subtractions/{subtraction_.id}/files/{filename}", path, "unknown"
+            f"/subtractions/{subtraction_.id}/files/{filename}", path, "unknown",
         )
 
         log.info("Finished uploading subtraction file")
diff --git a/virtool_workflow/data/uploads.py b/virtool_workflow/data/uploads.py
index 40638794b..2c7cb1b35 100644
--- a/virtool_workflow/data/uploads.py
+++ b/virtool_workflow/data/uploads.py
@@ -18,14 +18,13 @@ async def download(self, upload_id: int, path: Path):
 
 @fixture
 async def uploads(_api: APIClient) -> WFUploads:
-    """
-    Provides access to files that have been uploaded to the Virtool instance.
+    """Provides access to files that have been uploaded to the Virtool instance.
 
     Files can be downloaded into the workflow environment be calling
     :meth:`.WFUploads.download`.
 
     Example:
-
+    -------
     .. code-block:: python
 
         @step
diff --git a/virtool_workflow/decorators.py b/virtool_workflow/decorators.py
index a620fbe7a..d4d7f7bc4 100644
--- a/virtool_workflow/decorators.py
+++ b/virtool_workflow/decorators.py
@@ -6,8 +6,7 @@
 
 
 def step(func: Callable = None, *, name: str | None = None) -> Callable:
-    """
-    Mark a function as a workflow step function.
+    """Mark a function as a workflow step function.
 
     :param func: the workflow step function
     :param name: the display name of the workflow step. A name
@@ -23,13 +22,11 @@ def step(func: Callable = None, *, name: str | None = None) -> Callable:
 
 
 def collect(module: ModuleType) -> Workflow:
-    """
-    Build a :class:`.Workflow` object from a workflow module.
+    """Build a :class:`.Workflow` object from a workflow module.
 
     :param module: A workflow module
     :return: A workflow object
     """
-
     workflow = Workflow()
 
     markers = [
diff --git a/virtool_workflow/errors.py b/virtool_workflow/errors.py
index 543c89457..840a4745a 100644
--- a/virtool_workflow/errors.py
+++ b/virtool_workflow/errors.py
@@ -4,7 +4,6 @@
 class IllegalJobArguments(ValueError):
     """The `job.args` dict is in an illegal state."""
 
-    ...
 
 
 class InsufficientJobRights(Exception):
@@ -14,7 +13,7 @@ class InsufficientJobRights(Exception):
 class JobAlreadyAcquired(Exception):
     def __init__(self, job_id: str):
         super(JobAlreadyAcquired, self).__init__(
-            f"Job {job_id} is has already been acquired."
+            f"Job {job_id} is has already been acquired.",
         )
 
 
@@ -25,40 +24,33 @@ class JobAlreadyFinalized(Exception):
 class JobsAPIError(Exception):
     """A base exception for errors due to HTTP errors from the jobs API."""
 
-    ...
 
 
 class JobsAPIBadRequest(JobsAPIError):
     """A ``400 Bad Request`` response from the jobs API."""
 
     status = 400
-    ...
 
 
 class JobsAPIForbidden(JobsAPIError):
     status = 403
-    ...
 
 
 class JobsAPINotFound(JobsAPIError):
     status = 404
-    ...
 
 
 class JobsAPIConflict(JobsAPIError):
     status = 409
-    ...
 
 
 class JobsAPIServerError(JobsAPIError):
     status = 500
-    ...
 
 
 class MissingJobArgument(ValueError):
     """The `job.args` dict is missing a required key for some funcionality."""
 
-    ...
 
 
 class NotFound(KeyError):
diff --git a/virtool_workflow/hooks.py b/virtool_workflow/hooks.py
index c5ac95530..b9d462387 100644
--- a/virtool_workflow/hooks.py
+++ b/virtool_workflow/hooks.py
@@ -1,5 +1,4 @@
-"""
-Hooks provide a way to do things when events happen during the workflow lifecycle.
+"""Hooks provide a way to do things when events happen during the workflow lifecycle.
 """
 
 from virtool_workflow.runtime.hook import Hook
@@ -126,8 +125,7 @@ async def do_something_on_finish():
 
 
 def cleanup_builtin_status_hooks():
-    """
-    Clear callbacks for built-in status hooks.
+    """Clear callbacks for built-in status hooks.
 
     This prevents carryover of hooks between tests. Carryover won't be encountered in
     production because workflow processes exit after one run.
diff --git a/virtool_workflow/pytest_plugin/data.py b/virtool_workflow/pytest_plugin/data.py
index b6a500beb..12bf2c468 100644
--- a/virtool_workflow/pytest_plugin/data.py
+++ b/virtool_workflow/pytest_plugin/data.py
@@ -15,8 +15,8 @@
 )
 from virtool_core.models.subtraction import (
     Subtraction,
-    SubtractionNested,
     SubtractionFile,
+    SubtractionNested,
 )
 
 from virtool_workflow.pytest_plugin.utils import SUBTRACTION_FILENAMES
@@ -55,9 +55,9 @@ class Data:
     """An un-finalized subtraction for testing subtraction creation workflows."""
 
 
-@pytest.fixture
+@pytest.fixture()
 def data(
-    virtool_workflow_example_path: Path, static_datetime: datetime.datetime
+    virtool_workflow_example_path: Path, static_datetime: datetime.datetime,
 ) -> Data:
     class AnalysisFactory(ModelFactory):
         __model__ = Analysis
diff --git a/virtool_workflow/pytest_plugin/subprocess.py b/virtool_workflow/pytest_plugin/subprocess.py
index 25bbf6e65..d2cc3fbb0 100644
--- a/virtool_workflow/pytest_plugin/subprocess.py
+++ b/virtool_workflow/pytest_plugin/subprocess.py
@@ -3,6 +3,6 @@
 import virtool_workflow.runtime.run_subprocess
 
 
-@pytest.fixture
+@pytest.fixture()
 def run_subprocess() -> virtool_workflow.runtime.run_subprocess.RunSubprocess:
     return virtool_workflow.runtime.run_subprocess.run_subprocess()
diff --git a/virtool_workflow/runtime/discover.py b/virtool_workflow/runtime/discover.py
index 8bf8bdfac..026348d05 100644
--- a/virtool_workflow/runtime/discover.py
+++ b/virtool_workflow/runtime/discover.py
@@ -1,6 +1,6 @@
 import sys
 from importlib import import_module
-from importlib.util import spec_from_file_location, module_from_spec
+from importlib.util import module_from_spec, spec_from_file_location
 from pathlib import Path
 from types import ModuleType
 
@@ -13,8 +13,7 @@
 
 
 def discover_workflow(path: Path) -> Workflow:
-    """
-    Find an instance of :class:`.Workflow` in the python module located at the given
+    """Find an instance of :class:`.Workflow` in the python module located at the given
     path.
 
     :param path: The path to a Python module.
@@ -32,8 +31,7 @@ def discover_workflow(path: Path) -> Workflow:
 
 
 def load_builtin_fixtures():
-    """
-    Load built-in fixtures.
+    """Load built-in fixtures.
 
     This function is called before any fixtures defined in a workflow's
     ``fixtures.py`` file. It is used to provide built-in fixtures that are
@@ -59,8 +57,7 @@ def load_custom_fixtures():
 
 
 def load_workflow_from_file() -> Workflow:
-    """
-    Load a workflow from a Python file at ``./workflow.py`` and return a :class:`.Workflow` object.
+    """Load a workflow from a Python file at ``./workflow.py`` and return a :class:`.Workflow` object.
 
     :raises FileNotFoundError: If no workflow.py file is found.
     :return: The workflow.
@@ -75,8 +72,7 @@ def load_workflow_from_file() -> Workflow:
 
 
 def import_module_from_file(module_name: str, path: Path) -> ModuleType:
-    """
-    Import a module from a file.
+    """Import a module from a file.
 
     The parent directory of `path` will also be added to `sys.path` prior to importing.
     This ensures that modules and packages defined in that directory can be properly
diff --git a/virtool_workflow/runtime/hook.py b/virtool_workflow/runtime/hook.py
index f8d7998d7..bc76e3a2f 100644
--- a/virtool_workflow/runtime/hook.py
+++ b/virtool_workflow/runtime/hook.py
@@ -16,8 +16,7 @@ class Hook:
     """Used to hook into the workflow lifecycle."""
 
     def __init__(self, hook_name: str):
-        """
-        A set of functions to be called as a group upon a particular event.
+        """A set of functions to be called as a group upon a particular event.
 
         The signature of any functions added via :func:`Hook.callback` or
         :func:`Hook.__call__` are validated to match the types provided.
@@ -31,8 +30,7 @@ def __init__(self, hook_name: str):
         self.clear = self.callbacks.clear
 
     def __call__(self, callback_: Callable = None, until=None, once=False):
-        """
-        Add a callback function to this Hook that will be called when the hook is
+        """Add a callback function to this Hook that will be called when the hook is
         triggered.
 
         :param callback_: The callback function to register.
@@ -75,8 +73,7 @@ def remove_callback():
         return _temporary_callback
 
     async def trigger(self, scope: FixtureScope, suppress=False, **kwargs) -> list[Any]:
-        """
-        Trigger the hook.
+        """Trigger the hook.
 
         Bind fixtures from `scope` to each callback function and invoke them.
 
@@ -122,7 +119,7 @@ async def call_callback(callback):
                 return await callback(*args, **kwargs)
 
         results = await gather(
-            *[call_callback(callback) for callback in callbacks], return_exceptions=True
+            *[call_callback(callback) for callback in callbacks], return_exceptions=True,
         )
 
         for error in results:
diff --git a/virtool_workflow/runtime/path.py b/virtool_workflow/runtime/path.py
index 086c83bbc..dd9d6d3c6 100644
--- a/virtool_workflow/runtime/path.py
+++ b/virtool_workflow/runtime/path.py
@@ -1,7 +1,7 @@
 import asyncio
 from contextlib import asynccontextmanager
-from shutil import rmtree
 from pathlib import Path
+from shutil import rmtree
 
 from virtool_workflow.runtime.config import RunConfig
 
diff --git a/virtool_workflow/runtime/ping.py b/virtool_workflow/runtime/ping.py
index a0afbf2c2..2f6e7d94f 100644
--- a/virtool_workflow/runtime/ping.py
+++ b/virtool_workflow/runtime/ping.py
@@ -35,8 +35,7 @@ async def _ping_periodically(api: APIClient, job_id: str):
 
 @asynccontextmanager
 async def ping_periodically(api: APIClient, job_id: str):
-    """
-    Ping the API to keep the job alive.
+    """Ping the API to keep the job alive.
 
     While the context manager is open, a task runs that pings the API every 5 seconds.
     When the context manager is closed, the task is cleanly cancelled.
diff --git a/virtool_workflow/runtime/run.py b/virtool_workflow/runtime/run.py
index bf059724e..90ccf9a77 100644
--- a/virtool_workflow/runtime/run.py
+++ b/virtool_workflow/runtime/run.py
@@ -18,20 +18,20 @@
 from virtool_workflow.hooks import (
     cleanup_builtin_status_hooks,
     on_cancelled,
-    on_success,
-    on_step_start,
-    on_terminated,
     on_error,
     on_failure,
-    on_result,
     on_finish,
-    on_workflow_start,
+    on_result,
     on_step_finish,
+    on_step_start,
+    on_success,
+    on_terminated,
+    on_workflow_start,
 )
 from virtool_workflow.runtime.config import RunConfig
 from virtool_workflow.runtime.discover import (
-    load_custom_fixtures,
     load_builtin_fixtures,
+    load_custom_fixtures,
     load_workflow_from_file,
 )
 from virtool_workflow.runtime.events import Events
@@ -48,8 +48,7 @@
 
 
 def configure_status_hooks():
-    """
-    Configure built-in job status hooks.
+    """Configure built-in job status hooks.
 
     Push status updates to API when various lifecycle hooks are triggered.
 
@@ -77,8 +76,7 @@ async def handle_success(push_status):
 
 
 async def execute(workflow: Workflow, scope: FixtureScope, events: Events):
-    """
-    Execute a workflow.
+    """Execute a workflow.
 
     :param workflow: The workflow to execute
     :param scope: The :class:`FixtureScope` to use for fixture injection
@@ -118,7 +116,7 @@ async def execute(workflow: Workflow, scope: FixtureScope, events: Events):
 
             if not events.terminated.is_set():
                 logger.warning(
-                    "workflow terminated without sigterm. this should not happen."
+                    "workflow terminated without sigterm. this should not happen.",
                 )
 
             await asyncio.gather(
@@ -162,7 +160,7 @@ async def run_workflow(
     job = await acquire_job_by_id(config.jobs_api_connection_string, job_id)
 
     async with api_client(
-        config.jobs_api_connection_string, job.id, job.key
+        config.jobs_api_connection_string, job.id, job.key,
     ) as api, FixtureScope() as scope:
         # These fixtures should not be used directly by the workflow. They are used
         # by other built-in fixtures.
@@ -200,8 +198,7 @@ async def start_runtime(
     work_path: Path,
     workflow_loader: Callable[[], Workflow] = load_workflow_from_file,
 ):
-    """
-    Start the workflow runtime.
+    """Start the workflow runtime.
 
     The runtime loads the workflow and fixtures. It then waits for a job ID to be pushed
     to the configured Redis list.
@@ -261,7 +258,7 @@ async def start_runtime(
             job_id,
             workflow,
             events,
-        )
+        ),
     )
 
     def terminate_workflow(*_):
@@ -278,7 +275,7 @@ def cancel_workflow(*_):
 
     async with configure_redis(redis_connection_string) as redis:
         cancellation_task = asyncio.create_task(
-            wait_for_cancellation(redis, job_id, cancel_workflow)
+            wait_for_cancellation(redis, job_id, cancel_workflow),
         )
 
         await run_workflow_task
diff --git a/virtool_workflow/runtime/run_subprocess.py b/virtool_workflow/runtime/run_subprocess.py
index f08668452..1a1717e22 100644
--- a/virtool_workflow/runtime/run_subprocess.py
+++ b/virtool_workflow/runtime/run_subprocess.py
@@ -15,12 +15,11 @@
 
 class LineOutputHandler(Protocol):
     async def __call__(self, line: str):
-        """
-        Handle input from stdin, or stderr, line by line.
+        """Handle input from stdin, or stderr, line by line.
 
         :param line: A line of output from the stream.
         """
-        raise NotImplementedError()
+        raise NotImplementedError
 
 
 class RunSubprocess(Protocol):
@@ -32,8 +31,7 @@ async def __call__(
         stderr_handler: LineOutputHandler | None = None,
         stdout_handler: LineOutputHandler | None = None,
     ) -> Process:
-        """
-        Run a shell command in a subprocess.
+        """Run a shell command in a subprocess.
 
         :param command: A shell command
         :param stdout_handler: A function to handle stdout output line by line
@@ -43,14 +41,13 @@ async def __call__(
         :raise SubprocessFailed: The subprocess has exited with a non-zero exit code
         :return: An :class:`.Process` instance
         """
-        raise NotImplementedError()
+        raise NotImplementedError
 
 
 async def watch_pipe(
-    stream: asyncio.StreamReader, handler: Callable[[bytes], Awaitable[None]]
+    stream: asyncio.StreamReader, handler: Callable[[bytes], Awaitable[None]],
 ):
-    """
-    Watch the stdout or stderr stream and pass lines to the `handler` callback function.
+    """Watch the stdout or stderr stream and pass lines to the `handler` callback function.
 
     :param stream: a stdout or stderr file object
     :param handler: a handler coroutine for output lines
@@ -127,7 +124,7 @@ async def _stderr_handler(line):
     if process.returncode not in [0, 15, -15]:
         raise SubprocessFailed(
             f"{command[0]} failed with exit code {process.returncode}\n"
-            f"arguments: {command}\n"
+            f"arguments: {command}\n",
         )
 
     log.info(
diff --git a/virtool_workflow/runtime/sentry.py b/virtool_workflow/runtime/sentry.py
index 48eede0c4..9c393f5e6 100644
--- a/virtool_workflow/runtime/sentry.py
+++ b/virtool_workflow/runtime/sentry.py
@@ -9,8 +9,7 @@
 
 
 def configure_sentry(dsn: str):
-    """
-    Initialize Sentry for log aggregation.
+    """Initialize Sentry for log aggregation.
     """
     if dsn:
         logger.info("initializing sentry", dsn=f"{dsn[:15]}...")
@@ -20,7 +19,7 @@ def configure_sentry(dsn: str):
             integrations=[
                 LoggingIntegration(
                     event_level=logging.WARNING,
-                )
+                ),
             ],
             release=pkg_resources.get_distribution("virtool-workflow").version,
             traces_sample_rate=0.2,
diff --git a/virtool_workflow/utils.py b/virtool_workflow/utils.py
index f140749f8..ad0b200fd 100644
--- a/virtool_workflow/utils.py
+++ b/virtool_workflow/utils.py
@@ -1,8 +1,9 @@
 import asyncio
+import tarfile
+from collections.abc import Callable
 from functools import wraps
 from inspect import iscoroutinefunction
 from pathlib import Path
-from typing import Callable
 
 
 def coerce_to_coroutine_function(func: Callable):
@@ -19,3 +20,13 @@ async def _func(*args, **kwargs):
 
 async def make_directory(path: Path):
     await asyncio.to_thread(path.mkdir, exist_ok=True, parents=True)
+
+
+def untar(path: Path, target_path: Path):
+    with tarfile.open(path, "r:gz") as tar:
+        tar.extractall(target_path)
+
+
+def move_all_model_files(source_path: Path, target_path: Path):
+    for file in source_path.iterdir():
+        file.rename(target_path / file.name)
diff --git a/virtool_workflow/workflow.py b/virtool_workflow/workflow.py
index 5105a6573..9918271aa 100644
--- a/virtool_workflow/workflow.py
+++ b/virtool_workflow/workflow.py
@@ -2,21 +2,20 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field
-from typing import Callable, Optional, Awaitable, Any
+from typing import Any, Awaitable, Callable, Optional
 
 from virtool_workflow.utils import coerce_to_coroutine_function
 
 
 @dataclass
 class Workflow:
-    """
-    A step-wise, long-running operation.
+    """A step-wise, long-running operation.
     """
 
     steps: list[WorkflowStep] = field(default_factory=list)
 
     def step(
-        self, step: Optional[Callable] = None, *, name: str | None = None
+        self, step: Optional[Callable] = None, *, name: str | None = None,
     ) -> Callable:
         """Decorator for adding a step to the workflow."""
         if step is None:
@@ -33,8 +32,7 @@ def _decorator(func: Callable):
 
 @dataclass(frozen=True)
 class WorkflowStep:
-    """
-    Metadata for a workflow step.
+    """Metadata for a workflow step.
 
     :param name: The presentation name for the step.
     :param description: The description of the step.
@@ -53,8 +51,7 @@ def from_callable(
         display_name: str = None,
         description: str = None,
     ) -> WorkflowStep:
-        """
-        Create a WorkflowStep from a callable.
+        """Create a WorkflowStep from a callable.
 
         :param func: The callable to be used.
         :param display_name: The display name to be used, if None then a display name
@@ -82,8 +79,7 @@ async def __call__(self, *args, **kwargs):
 
 
 def _get_description_from_docstring(func: Callable[..., Any]) -> str:
-    """
-    Extract the first line of the docstring as a description for a step function.
+    """Extract the first line of the docstring as a description for a step function.
 
     :param func: The step function to get the description for
     :raise ValueError: When `call` does not have a docstring