diff --git a/.python-version b/.python-version
index 3a4f41e..24ee5b1 100644
--- a/.python-version
+++ b/.python-version
@@ -1 +1 @@
-3.13
\ No newline at end of file
+3.13
diff --git a/pyproject.toml b/pyproject.toml
index 1ba7de4..dfc1494 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,9 +36,6 @@ Repository = "https://github.com/Clinical-Genomics/stranger"
 Changelog = "https://github.com/Clinical-Genomics/stranger/blob/main/CHANGELOG.md"
 "Bug Tracker" = "https://github.com/Clinical-Genomics/stranger/issues"
 
-[project.optional-dependencies]
-test = ["pytest","pytest-cov"]
-dev = ["ruff>=0.7.2"]
 
 [project.scripts]
 stranger = "stranger.cli:cli"
@@ -54,3 +51,13 @@ target-version = ['py313']
 [tool.ruff]
 src = ["stranger", "tests", "scripts"]
 line-length = 100
+
+[dependency-groups]
+dev = [
+    "pytest-cov>=4.1.0",
+    "pytest>=7.4.4",
+]
+lint = [
+    "black>=23.3.0",
+    "ruff>=0.8.0",
+]
diff --git a/uv.lock b/uv.lock
index dfd1b84..98ec358 100644
--- a/uv.lock
+++ b/uv.lock
@@ -5,6 +5,48 @@ resolution-markers = [
     "python_full_version >= '3.8' and sys_platform == 'win32'",
 ]
 
+[[package]]
+name = "black"
+version = "23.3.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "click" },
+    { name = "mypy-extensions" },
+    { name = "packaging" },
+    { name = "pathspec" },
+    { name = "platformdirs" },
+    { name = "tomli", marker = "python_full_version < '3.11'" },
+    { name = "typed-ast", marker = "python_full_version < '3.8' and implementation_name == 'cpython'" },
+    { name = "typing-extensions", marker = "python_full_version < '3.10'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/d6/36/66370f5017b100225ec4950a60caeef60201a10080da57ddb24124453fba/black-23.3.0.tar.gz", hash = "sha256:1c7b8d606e728a41ea1ccbd7264677e494e87cf630e399262ced92d4a8dac940", size = 582156 }
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+    { url = "https://files.pythonhosted.org/packages/06/1e/273d610249f0335afb1ddb03664a03223f4826e3d1a95170a0142cb19fb4/black-23.3.0-cp39-cp39-win_amd64.whl", hash = "sha256:6b39abdfb402002b8a7d030ccc85cf5afff64ee90fa4c5aebc531e3ad0175ddb", size = 1286299 },
+    { url = "https://files.pythonhosted.org/packages/ad/e7/4642b7f462381799393fbad894ba4b32db00870a797f0616c197b07129a9/black-23.3.0-py3-none-any.whl", hash = "sha256:ec751418022185b0c1bb7d7736e6933d40bbb14c14a0abcf9123d1b159f98dd4", size = 180965 },
+]
+
 [[package]]
 name = "click"
 version = "8.1.7"
@@ -167,6 +209,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/ef/a6/62565a6e1cf69e10f5727360368e451d4b7f58beeac6173dc9db836a5b46/iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374", size = 5892 },
 ]
 
+[[package]]
+name = "mypy-extensions"
+version = "1.0.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/98/a4/1ab47638b92648243faf97a5aeb6ea83059cc3624972ab6b8d2316078d3f/mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782", size = 4433 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2a/e2/5d3f6ada4297caebe1a2add3b126fe800c96f56dbe5d1988a2cbe0b267aa/mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d", size = 4695 },
+]
+
 [[package]]
 name = "packaging"
 version = "24.0"
@@ -176,6 +227,27 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/49/df/1fceb2f8900f8639e278b056416d49134fb8d84c5942ffaa01ad34782422/packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5", size = 53488 },
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+[[package]]
+name = "pathspec"
+version = "0.11.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/a0/2a/bd167cdf116d4f3539caaa4c332752aac0b3a0cc0174cdb302ee68933e81/pathspec-0.11.2.tar.gz", hash = "sha256:e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3", size = 47032 }
+wheels = [
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+]
+
+[[package]]
+name = "platformdirs"
+version = "4.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "typing-extensions", marker = "python_full_version < '3.8'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/31/28/e40d24d2e2eb23135f8533ad33d582359c7825623b1e022f9d460def7c05/platformdirs-4.0.0.tar.gz", hash = "sha256:cb633b2bcf10c51af60beb0ab06d2f1d69064b43abf4c185ca6b28865f3f9731", size = 19914 }
+wheels = [
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+
 [[package]]
 name = "pluggy"
 version = "1.2.0"
@@ -288,27 +360,27 @@ wheels = [
 
 [[package]]
 name = "ruff"
-version = "0.7.2"
+version = "0.8.0"
 source = { registry = "https://pypi.org/simple" }
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 [[package]]
@@ -322,24 +394,32 @@ dependencies = [
     { name = "pyyaml" },
 ]
 
-[package.optional-dependencies]
+[package.dev-dependencies]
 dev = [
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-]
-test = [
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     { name = "pytest-cov" },
 ]
+lint = [
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+    { name = "ruff" },
+]
 
 [package.metadata]
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     { name = "coloredlogs" },
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     { name = "pyyaml" },
-    { name = "ruff", marker = "extra == 'dev'", specifier = ">=0.7.2" },
+]
+
+[package.metadata.requires-dev]
+dev = [
+    { name = "pytest", specifier = ">=7.4.4" },
+    { name = "pytest-cov", specifier = ">=4.1.0" },
+]
+lint = [
+    { name = "black", specifier = ">=23.3.0" },
+    { name = "ruff", specifier = ">=0.8.0" },
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