From 6946532a4992e41c416c187c8e1be5bff7565255 Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Wed, 12 Jun 2024 12:29:09 -0700
Subject: [PATCH] feat: support jobs without `rights` field

* Support jobs without `rights` field.
* Pin Python at 3.12.3.
---
 Dockerfile             |    8 +-
 poetry.lock            | 1127 +++++++++++++++++-----------------------
 pyproject.toml         |   26 +-
 tests/test_utils.py    |   13 +-
 tests/test_workflow.py |   13 +-
 utils.py               |    5 +-
 6 files changed, 524 insertions(+), 668 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 45ddd5a..0863e76 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -26,7 +26,7 @@ RUN ./configure --prefix /build/samtools
 RUN make
 RUN make install
 
-FROM python:3.10-bookworm as rbuild
+FROM python:3.12.3-bookworm as rbuild
 WORKDIR /build
 RUN apt-get update && apt-get install -y libdeflate0 r-base r-cran-littler
 RUN R -e "install.packages('BiocManager')"
@@ -36,15 +36,15 @@ RUN R -e "install.packages(c('data.table', 'dplyr', 'mltools', 'randomForest', '
 COPY ./iimi ./iimi
 RUN R -e "install.packages('iimi', repos = NULL, type = 'source')"
 
-FROM python:3.10-bookworm as base
+FROM python:3.12.3-bookworm as base
 WORKDIR /app
 RUN apt-get update && apt-get install -y libdeflate0 r-base r-cran-littler
 COPY --from=prep /build/bowtie2/* /usr/local/bin/
 COPY --from=prep /build/pigz-2.8/pigz /usr/local/bin/pigz
 COPY --from=prep /build/samtools/bin/samtools /usr/local/bin/samtools
 COPY --from=prep /build/skewer /usr/local/bin/
-RUN curl -sSL https://install.python-poetry.org | python - --version 1.7.1
-ENV PATH="/root/.local/bin:${PATH}"
+RUN curl -sSL https://install.python-poetry.org | python3 - --version 1.8.3
+ENV PATH="/root/.local/bin:$PATH"
 COPY poetry.lock pyproject.toml ./
 RUN poetry install --without dev --no-root
 COPY --from=rbuild /usr/local/lib/R/site-library /usr/local/lib/R/site-library
diff --git a/poetry.lock b/poetry.lock
index 53b7138..a5f9d5e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "aiofiles"
@@ -13,92 +13,91 @@ files = [
 
 [[package]]
 name = "aiohttp"
-version = "3.9.1"
+version = "3.9.5"
 description = "Async http client/server framework (asyncio)"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
 aiosignal = ">=1.1.2"
-async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
@@ -107,21 +106,6 @@ yarl = ">=1.0,<2.0"
 [package.extras]
 speedups = ["Brotli", "aiodns", "brotlicffi"]
 
-[[package]]
-name = "aioredis"
-version = "1.3.1"
-description = "asyncio (PEP 3156) Redis support"
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-
-[package.dependencies]
-async-timeout = "*"
-hiredis = "*"
-
 [[package]]
 name = "aiosignal"
 version = "1.3.1"
@@ -155,17 +139,6 @@ types-python-dateutil = ">=2.8.10"
 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 = "4.0.3"
-description = "Timeout context manager for asyncio programs"
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-
 [[package]]
 name = "attrs"
 version = "23.2.0"
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 python-versions = ">=3.8"
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@@ -221,13 +199,13 @@ numpy = "*"
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.6.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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+    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
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 ]
 
 [[package]]
@@ -274,32 +252,33 @@ tests = ["check-manifest (>=0.25)", "coverage (>=4.0)", "isort (>=4.2.2)", "mock
 
 [[package]]
 name = "dnspython"
-version = "2.4.2"
+version = "2.6.1"
 description = "DNS toolkit"
 optional = false
-python-versions = ">=3.8,<4.0"
+python-versions = ">=3.8"
 files = [
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-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,<0.23)"]
-wmi = ["wmi (>=1.5.1,<2.0.0)"]
+dev = ["black (>=23.1.0)", "coverage (>=7.0)", "flake8 (>=7)", "mypy (>=1.8)", "pylint (>=3)", "pytest (>=7.4)", "pytest-cov (>=4.1.0)", "sphinx (>=7.2.0)", "twine (>=4.0.0)", "wheel (>=0.42.0)"]
+dnssec = ["cryptography (>=41)"]
+doh = ["h2 (>=4.1.0)", "httpcore (>=1.0.0)", "httpx (>=0.26.0)"]
+doq = ["aioquic (>=0.9.25)"]
+idna = ["idna (>=3.6)"]
+trio = ["trio (>=0.23)"]
+wmi = ["wmi (>=1.5.1)"]
 
 [[package]]
 name = "email-validator"
-version = "2.1.0.post1"
+version = "2.1.1"
 description = "A robust email address syntax and deliverability validation library."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -325,29 +304,15 @@ typing-extensions = ">=3.7.4.3"
 all = ["sphinx (>=3.4.0)", "sphinx-jinja2-compat (>=0.1.1)", "sphinx-toolbox (>=2.16.0)"]
 sphinx = ["sphinx (>=3.4.0)", "sphinx-jinja2-compat (>=0.1.1)", "sphinx-toolbox (>=2.16.0)"]
 
-[[package]]
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-description = "Backport of PEP 654 (exception groups)"
-optional = false
-python-versions = ">=3.7"
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-]
-
-[package.extras]
-test = ["pytest (>=6)"]
-
 [[package]]
 name = "faker"
-version = "22.2.0"
+version = "25.8.0"
 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]
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-
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 name = "idna"
-version = "3.6"
+version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
 files = [
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 [[package]]
@@ -581,13 +428,13 @@ files = [
 
 [[package]]
 name = "motor"
-version = "3.3.2"
+version = "3.4.0"
 description = "Non-blocking MongoDB driver for Tornado or asyncio"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -600,7 +447,7 @@ 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)"]
+test = ["aiohttp (!=3.8.6)", "mockupdb", "motor[encryption]", "pytest (>=7)", "tornado (>=5)"]
 zstd = ["pymongo[zstd] (>=4.5,<5)"]
 
 [[package]]
@@ -623,211 +470,223 @@ motor = ["dnspython (>=2.3.0)", "motor (>=3.0.0)"]
 
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 [package.dependencies]
 dnspython = ">=1.16.0,<3.0.0"
 
 [package.extras]
-aws = ["pymongo-auth-aws (<2.0.0)"]
-encryption = ["certifi", "pymongo[aws]", "pymongocrypt (>=1.6.0,<2.0.0)"]
+aws = ["pymongo-auth-aws (>=1.1.0,<2.0.0)"]
+encryption = ["certifi", "pymongo-auth-aws (>=1.1.0,<2.0.0)", "pymongocrypt (>=1.6.0,<2.0.0)"]
 gssapi = ["pykerberos", "winkerberos (>=0.5.0)"]
 ocsp = ["certifi", "cryptography (>=2.5)", "pyopenssl (>=17.2.0)", "requests (<3.0.0)", "service-identity (>=18.1.0)"]
 snappy = ["python-snappy"]
@@ -1044,47 +880,26 @@ files = [
 
 [package.dependencies]
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
-exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<2.0"
-tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
-[[package]]
-name = "pytest-aiohttp"
-version = "1.0.5"
-description = "Pytest plugin for aiohttp support"
-optional = false
-python-versions = ">=3.7"
-files = [
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-]
-
-[package.dependencies]
-aiohttp = ">=3.8.1"
-pytest = ">=6.1.0"
-pytest-asyncio = ">=0.17.2"
-
-[package.extras]
-testing = ["coverage (==6.2)", "mypy (==0.931)"]
-
 [[package]]
 name = "pytest-asyncio"
-version = "0.23.3"
+version = "0.23.7"
 description = "Pytest support for asyncio"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pytest-asyncio-0.23.3.tar.gz", hash = "sha256:af313ce900a62fbe2b1aed18e37ad757f1ef9940c6b6a88e2954de38d6b1fb9f"},
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+    {file = "pytest_asyncio-0.23.7-py3-none-any.whl", hash = "sha256:009b48127fbe44518a547bddd25611551b0e43ccdbf1e67d12479f569832c20b"},
+    {file = "pytest_asyncio-0.23.7.tar.gz", hash = "sha256:5f5c72948f4c49e7db4f29f2521d4031f1c27f86e57b046126654083d4770268"},
 ]
 
 [package.dependencies]
-pytest = ">=7.0.0"
+pytest = ">=7.0.0,<9"
 
 [package.extras]
 docs = ["sphinx (>=5.3)", "sphinx-rtd-theme (>=1.0)"]
@@ -1092,70 +907,116 @@ testing = ["coverage (>=6.2)", "hypothesis (>=5.7.1)"]
 
 [[package]]
 name = "pytest-mock"
-version = "3.12.0"
+version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pytest-mock-3.14.0.tar.gz", hash = "sha256:2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0"},
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 ]
 
 [package.dependencies]
-pytest = ">=5.0"
+pytest = ">=6.2.5"
 
 [package.extras]
 dev = ["pre-commit", "pytest-asyncio", "tox"]
 
 [[package]]
 name = "python-dateutil"
-version = "2.8.2"
+version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
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 ]
 
 [package.dependencies]
 six = ">=1.5"
 
+[[package]]
+name = "redis"
+version = "5.0.5"
+description = "Python client for Redis database and key-value store"
+optional = false
+python-versions = ">=3.7"
+files = [
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+
+[[package]]
+name = "ruff"
+version = "0.4.8"
+description = "An extremely fast Python linter and code formatter, written in Rust."
+optional = false
+python-versions = ">=3.7"
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+
 [[package]]
 name = "sentry-sdk"
-version = "1.39.2"
+version = "2.5.1"
 description = "Python client for Sentry (https://sentry.io)"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
 certifi = "*"
-urllib3 = {version = ">=1.26.11", markers = "python_version >= \"3.6\""}
+urllib3 = ">=1.26.11"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.5)"]
+anthropic = ["anthropic (>=0.16)"]
 arq = ["arq (>=0.23)"]
 asyncpg = ["asyncpg (>=0.23)"]
 beam = ["apache-beam (>=2.12)"]
 bottle = ["bottle (>=0.12.13)"]
 celery = ["celery (>=3)"]
+celery-redbeat = ["celery-redbeat (>=2)"]
 chalice = ["chalice (>=1.16.0)"]
 clickhouse-driver = ["clickhouse-driver (>=0.2.0)"]
 django = ["django (>=1.8)"]
 falcon = ["falcon (>=1.4)"]
 fastapi = ["fastapi (>=0.79.0)"]
 flask = ["blinker (>=1.1)", "flask (>=0.11)", "markupsafe"]
-grpcio = ["grpcio (>=1.21.1)"]
+grpcio = ["grpcio (>=1.21.1)", "protobuf (>=3.8.0)"]
 httpx = ["httpx (>=0.16.0)"]
 huey = ["huey (>=2)"]
+huggingface-hub = ["huggingface-hub (>=0.22)"]
+langchain = ["langchain (>=0.0.210)"]
 loguru = ["loguru (>=0.5)"]
+openai = ["openai (>=1.0.0)", "tiktoken (>=0.3.0)"]
 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)"]
@@ -1196,112 +1057,102 @@ typing = ["mypy (>=1.4)", "rich", "twisted"]
 
 [[package]]
 name = "syrupy"
-version = "4.6.0"
+version = "4.6.1"
 description = "Pytest Snapshot Test Utility"
 optional = false
 python-versions = ">=3.8.1,<4"
 files = [
-    {file = "syrupy-4.6.0-py3-none-any.whl", hash = "sha256:747aae1bcf3cb3249e33b1e6d81097874d23615982d5686ebe637875b0775a1b"},
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+    {file = "syrupy-4.6.1-py3-none-any.whl", hash = "sha256:203e52f9cb9fa749cf683f29bd68f02c16c3bc7e7e5fe8f2fc59bdfe488ce133"},
+    {file = "syrupy-4.6.1.tar.gz", hash = "sha256:37a835c9ce7857eeef86d62145885e10b3cb9615bc6abeb4ce404b3f18e1bb36"},
 ]
 
 [package.dependencies]
-pytest = ">=7.0.0,<8.0.0"
-
-[[package]]
-name = "tomli"
-version = "2.0.1"
-description = "A lil' TOML parser"
-optional = false
-python-versions = ">=3.7"
-files = [
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-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
-]
+pytest = ">=7.0.0,<9.0.0"
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.8.19.20240106"
+version = "2.9.0.20240316"
 description = "Typing stubs for python-dateutil"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "types-python-dateutil-2.9.0.20240316.tar.gz", hash = "sha256:5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202"},
+    {file = "types_python_dateutil-2.9.0.20240316-py3-none-any.whl", hash = "sha256:6b8cb66d960771ce5ff974e9dd45e38facb81718cc1e208b10b1baccbfdbee3b"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.9.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.1.0"
+version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "virtool-core"
-version = "11.0.0"
+version = "14.0.1"
 description = "Core utilities for Virtool."
 optional = false
-python-versions = ">3.8,<3.13"
+python-versions = "<3.13,>=3.12"
 files = [
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 arrow = ">=1.2.2,<2.0.0"
 dictdiffer = "0.8.1"
-email-validator = ">=2.0.0.post2,<3.0.0"
+email-validator = ">=2.1.1,<3.0.0"
 enum-tools = ">=0.11.0,<0.12.0"
 motor = ">=3.1.2,<4.0.0"
 motor-types = ">=1.0.0b3,<2.0.0"
+orjson = ">=3.10.1,<4.0.0"
 pydantic = ">=1.8.2,<2.0.0"
+redis = ">=5.0.3,<6.0.0"
 structlog = ">=23.1.0,<24.0.0"
 
 [[package]]
 name = "virtool-workflow"
-version = "6.0.0a11"
+version = "7.1.0"
 description = "A framework for developing bioinformatics workflows for Virtool."
 optional = false
-python-versions = ">=3.10,<3.11"
+python-versions = "<3.13,>=3.12"
 files = [
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 [package.dependencies]
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 aiohttp = ">=3.8.1,<4.0.0"
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 biopython = ">=1.81,<2.0"
 click = ">=8.1.7,<9.0.0"
 orjson = ">=3.9.9,<4.0.0"
 pydantic-factories = ">=1.17.3,<2.0.0"
 pyfixtures = ">=1.0.0,<2.0.0"
-sentry-sdk = ">=1.5.7,<2.0.0"
-virtool-core = ">=11.0.0,<12.0.0"
+sentry-sdk = ">=2.3.1,<3.0.0"
+virtool-core = ">=14.0.0,<15.0.0"
 
 [[package]]
 name = "yarl"
@@ -1408,5 +1259,5 @@ multidict = ">=4.0"
 
 [metadata]
 lock-version = "2.0"
-python-versions = "~3.10"
-content-hash = "3ba8079a0ae461bbf24e61f3cc09fc14207cde6ba7e864c6c5ce353a428a9c49"
+python-versions = "~3.12"
+content-hash = "d838de288ef11231080491720d4281ce739ccf1cf04f922ee4811f20b629dc9f"
diff --git a/pyproject.toml b/pyproject.toml
index 3175e63..cede524 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,26 +1,28 @@
 [tool.poetry]
 name = "workflow-iimi"
-version = "0.1.0"
+version = "0.0.0"
 description = ""
-authors = ["Ian Boyes"]
+authors = ["Ian Boyes <igboyes@gmail.com>"]
 license = "MIT"
 
 [tool.poetry.dependencies]
-python = "~3.10"
-virtool-workflow = {version="^6.0.0a7", allow-prereleases=true}
-biopython = "^1.81"
-pydantic-factories = "^1.17.3"
+python = "~3.12"
+virtool-workflow = "^7.1.0"
+biopython = "^1.83"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.2"
 pytest-asyncio = "^0.23.2"
-pytest-aiohttp = "^1.0.5"
-syrupy = "^4.6.0"
 pytest-mock = "^3.12.0"
+ruff = "^0.4.8"
+syrupy = "^4.6.0"
+
+[tool.pytest.ini_options]
+asyncio_mode = "auto"
+
+[tool.ruff.lint]
+select = ["ALL"]
 
 [build-system]
-requires = ["poetry-core"]
+requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
-
-[tool.pytest.ini_options]
-markers = ["asyncio_mode: auto"]
diff --git a/tests/test_utils.py b/tests/test_utils.py
index d33b975..447d6a4 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -3,14 +3,18 @@
 
 from syrupy import SnapshotAssertion
 
-from utils import write_iimi_nucleotide_info, load_and_format_prediction_results
+from utils import load_and_format_prediction_results, write_iimi_nucleotide_info
 
 
 def test_write_iimi_nucleotide_info(
-    example_path: Path, logger, snapshot: SnapshotAssertion, work_path: Path
+    example_path: Path,
+    logger,
+    snapshot: SnapshotAssertion,
+    work_path: Path,
 ):
     shutil.copyfile(
-        example_path / "index" / "reference.json.gz", work_path / "reference.json.gz"
+        example_path / "index" / "reference.json.gz",
+        work_path / "reference.json.gz",
     )
 
     output_path = work_path / "nucleotide_info.csv"
@@ -37,6 +41,7 @@ def test_load_prediction_results(snapshot: SnapshotAssertion, work_path: Path):
     assert [
         obj.dict()
         for obj in load_and_format_prediction_results(
-            work_path / "reference.json.gz", output_path
+            work_path / "reference.json.gz",
+            output_path,
         )
     ] == snapshot
diff --git a/tests/test_workflow.py b/tests/test_workflow.py
index 712541a..1da5f44 100644
--- a/tests/test_workflow.py
+++ b/tests/test_workflow.py
@@ -23,7 +23,7 @@
 from workflow import build_all_otu_index, map_all_otus, predict
 
 
-@pytest.fixture
+@pytest.fixture()
 def analysis(data: Data, mocker) -> WFAnalysis:
     data.analysis.ready = False
 
@@ -40,7 +40,7 @@ def analysis(data: Data, mocker) -> WFAnalysis:
     return analysis
 
 
-@pytest.fixture
+@pytest.fixture()
 def index(data: Data, example_path: Path, work_path: Path) -> WFIndex:
     index_path = work_path / "indexes" / data.index.id
 
@@ -63,7 +63,7 @@ def index(data: Data, example_path: Path, work_path: Path) -> WFIndex:
     )
 
 
-@pytest.fixture
+@pytest.fixture()
 def ml(data: Data, example_path: Path, work_path: Path) -> WFMLModelRelease:
     path = work_path / "ml" / str(data.ml.id) / str(data.ml.model.id)
     path.mkdir(parents=True)
@@ -82,7 +82,7 @@ def ml(data: Data, example_path: Path, work_path: Path) -> WFMLModelRelease:
     return obj
 
 
-@pytest.fixture
+@pytest.fixture()
 def sample(data: Data, example_path: Path, work_path: Path) -> WFSample:
     sample_path = work_path / "samples" / data.sample.id
     sample_path.mkdir(parents=True)
@@ -102,7 +102,7 @@ def sample(data: Data, example_path: Path, work_path: Path) -> WFSample:
     )
 
 
-@pytest.mark.asyncio
+@pytest.mark.asyncio()
 async def test_workflow(
     analysis: WFAnalysis,
     example_path: Path,
@@ -116,7 +116,6 @@ async def test_workflow(
     work_path: Path,
 ):
     """Make sure the workflow runs without error."""
-
     all_otu_index_path = work_path / "all_otu_index"
     all_otu_index_path.mkdir()
 
@@ -167,7 +166,7 @@ async def test_workflow(
     assert analysis.upload_result.call_args[0] == snapshot
 
 
-@pytest.mark.asyncio
+@pytest.mark.asyncio()
 async def test_predict(
     analysis: WFAnalysis,
     example_path: Path,
diff --git a/utils.py b/utils.py
index 953a462..56562ec 100644
--- a/utils.py
+++ b/utils.py
@@ -183,7 +183,8 @@ def load_virus_annotations(
 
 
 def load_and_format_prediction_results(
-    reference_json_path: Path, output_path: Path,
+    reference_json_path: Path,
+    output_path: Path,
 ) -> list[PredictionHit]:
     """Load IIMI results into a list of ``PredictionHit`` objects.
 
@@ -352,5 +353,3 @@ def write_iimi_nucleotide_info(reference_json_path: Path, output_path: Path, log
 def untar(path: Path, target_path: Path):
     with tarfile.open(path, "r:gz") as tar:
         tar.extractall(target_path)
-
-