From 30d7f96c73a0307779b9503160da50a2d9924e91 Mon Sep 17 00:00:00 2001
From: Matin Nuhamunada <matinnu@biosustain.dtu.dk>
Date: Mon, 20 Nov 2023 16:12:03 +0000
Subject: [PATCH] fix: pin snakemake to v7.31.1 and security updates

---
 poetry.lock    | 1039 ++++++++++++++++++++++++------------------------
 pyproject.toml |    2 +-
 2 files changed, 527 insertions(+), 514 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index bd0b48a..8b899dd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "appdirs"
@@ -24,20 +24,21 @@ files = [
 
 [[package]]
 name = "asttokens"
-version = "2.4.0"
+version = "2.4.1"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = "*"
 files = [
-    {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"},
-    {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"},
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
 ]
 
 [package.dependencies]
 six = ">=1.12.0"
 
 [package.extras]
-test = ["astroid", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "astunparse"
@@ -88,17 +89,18 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 
 [[package]]
 name = "babel"
-version = "2.13.0"
+version = "2.13.1"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"},
-    {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"},
+    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
+    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
 ]
 
 [package.dependencies]
 pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
+setuptools = {version = "*", markers = "python_version >= \"3.12\""}
 
 [package.extras]
 dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
@@ -187,35 +189,35 @@ css = ["tinycss2 (>=1.1.0,<1.3)"]
 
 [[package]]
 name = "blinker"
-version = "1.6.3"
+version = "1.7.0"
 description = "Fast, simple object-to-object and broadcast signaling"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "blinker-1.6.3-py3-none-any.whl", hash = "sha256:296320d6c28b006eb5e32d4712202dbcdcbf5dc482da298c2f44881c43884aaa"},
-    {file = "blinker-1.6.3.tar.gz", hash = "sha256:152090d27c1c5c722ee7e48504b02d76502811ce02e1523553b4cf8c8b3d3a8d"},
+    {file = "blinker-1.7.0-py3-none-any.whl", hash = "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9"},
+    {file = "blinker-1.7.0.tar.gz", hash = "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"},
 ]
 
 [[package]]
 name = "cachetools"
-version = "5.3.1"
+version = "5.3.2"
 description = "Extensible memoizing collections and decorators"
 optional = true
 python-versions = ">=3.7"
 files = [
-    {file = "cachetools-5.3.1-py3-none-any.whl", hash = "sha256:95ef631eeaea14ba2e36f06437f36463aac3a096799e876ee55e5cdccb102590"},
-    {file = "cachetools-5.3.1.tar.gz", hash = "sha256:dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b"},
+    {file = "cachetools-5.3.2-py3-none-any.whl", hash = "sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1"},
+    {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
+    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
 ]
 
 [[package]]
@@ -306,101 +308,101 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.0"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
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-    {file = "charset_normalizer-3.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0570d21da019941634a531444364f2482e8db0b3425fcd5ac0c36565a64142c8"},
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 [[package]]
@@ -430,22 +432,20 @@ files = [
 
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 name = "comm"
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+version = "0.2.0"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
 traitlets = ">=4"
 
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 test = ["pytest"]
-typing = ["mypy (>=0.990)"]
 
 [[package]]
 name = "configargparse"
@@ -541,34 +541,34 @@ toml = ["tomli"]
 
 [[package]]
 name = "cryptography"
-version = "41.0.4"
+version = "41.0.5"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -753,13 +753,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "2.0.0"
+version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
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 ]
 
 [package.extras]
@@ -767,13 +767,13 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fastjsonschema"
-version = "2.18.1"
+version = "2.19.0"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.extras]
@@ -781,19 +781,19 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
-version = "3.12.4"
+version = "3.13.1"
 description = "A platform independent file lock."
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
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-testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"]
-typing = ["typing-extensions (>=4.7.1)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
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+typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
 name = "flake8"
@@ -868,13 +868,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "gitdb"
-version = "4.0.10"
+version = "4.0.11"
 description = "Git Object Database"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -882,90 +882,85 @@ smmap = ">=3.0.1,<6"
 
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+version = "3.1.40"
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 [package.dependencies]
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 ]
 
 [package.extras]
@@ -988,13 +983,13 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve
 
 [[package]]
 name = "identify"
-version = "2.5.30"
+version = "2.5.32"
 description = "File identification library for Python"
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.30-py2.py3-none-any.whl", hash = "sha256:afe67f26ae29bab007ec21b03d4114f41316ab9dd15aa8736a167481e108da54"},
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 ]
 
 [package.extras]
@@ -1032,13 +1027,13 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.0"
+version = "6.1.1"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1061,13 +1056,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.25.2"
+version = "6.26.0"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "ipykernel-6.26.0.tar.gz", hash = "sha256:553856658eb8430bbe9653ea041a41bff63e9606fc4628873fc92a6cf3abd404"},
 ]
 
 [package.dependencies]
@@ -1230,13 +1225,13 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "4.19.1"
+version = "4.20.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1253,28 +1248,28 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.7.1"
+version = "2023.11.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jsonschema_specifications-2023.11.1.tar.gz", hash = "sha256:c9b234904ffe02f079bf91b14d79987faa685fd4b39c377a0996954c0090b9ca"},
 ]
 
 [package.dependencies]
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter-client"
-version = "8.4.0"
+version = "8.6.0"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jupyter_client-8.6.0.tar.gz", hash = "sha256:0642244bb83b4764ae60d07e010e15f0e2d275ec4e918a8f7b80fbbef3ca60c7"},
 ]
 
 [package.dependencies]
@@ -1291,13 +1286,13 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 
 [[package]]
 name = "jupyter-core"
-version = "5.4.0"
+version = "5.5.0"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_core-5.4.0-py3-none-any.whl", hash = "sha256:66e252f675ac04dcf2feb6ed4afb3cd7f68cf92f483607522dc251f32d471571"},
-    {file = "jupyter_core-5.4.0.tar.gz", hash = "sha256:e4b98344bb94ee2e3e6c4519a97d001656009f9cb2b7f2baf15b3c205770011d"},
+    {file = "jupyter_core-5.5.0-py3-none-any.whl", hash = "sha256:e11e02cd8ae0a9de5c6c44abf5727df9f2581055afe00b22183f621ba3585805"},
+    {file = "jupyter_core-5.5.0.tar.gz", hash = "sha256:880b86053bf298a8724994f95e99b99130659022a4f7f45f563084b6223861d3"},
 ]
 
 [package.dependencies]
@@ -1306,7 +1301,7 @@ pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_
 traitlets = ">=5.3"
 
 [package.extras]
-docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
 test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
@@ -1344,13 +1339,13 @@ toml = ["toml"]
 
 [[package]]
 name = "keyring"
-version = "24.2.0"
+version = "24.3.0"
 description = "Store and access your passwords safely."
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "keyring-24.2.0-py3-none-any.whl", hash = "sha256:4901caaf597bfd3bbd78c9a0c7c4c29fcd8310dab2cffefe749e916b6527acd6"},
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+    {file = "keyring-24.3.0-py3-none-any.whl", hash = "sha256:4446d35d636e6a10b8bce7caa66913dd9eca5fd222ca03a3d42c38608ac30836"},
+    {file = "keyring-24.3.0.tar.gz", hash = "sha256:e730ecffd309658a08ee82535a3b5ec4b4c8669a9be11efb66249d8e0aeb9a25"},
 ]
 
 [package.dependencies]
@@ -1362,9 +1357,9 @@ pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""}
 SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
-completion = ["shtab"]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+completion = ["shtab (>=1.1.0)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [[package]]
 name = "livereload"
@@ -1383,13 +1378,13 @@ tornado = {version = "*", markers = "python_version > \"2.7\""}
 
 [[package]]
 name = "markdown"
-version = "3.5"
+version = "3.5.1"
 description = "Python implementation of John Gruber's Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "Markdown-3.5-py3-none-any.whl", hash = "sha256:4afb124395ce5fc34e6d9886dab977fd9ae987fc6e85689f08278cf0c69d4bf3"},
-    {file = "Markdown-3.5.tar.gz", hash = "sha256:a807eb2e4778d9156c8f07876c6e4d50b5494c5665c4834f67b06459dfd877b3"},
+    {file = "Markdown-3.5.1-py3-none-any.whl", hash = "sha256:5874b47d4ee3f0b14d764324d2c94c03ea66bee56f2d929da9f2508d65e722dc"},
+    {file = "Markdown-3.5.1.tar.gz", hash = "sha256:b65d7beb248dc22f2e8a31fb706d93798093c308dc1aba295aedeb9d41a813bd"},
 ]
 
 [package.dependencies]
@@ -1450,6 +1445,16 @@ files = [
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     {file = "MarkupSafe-2.1.3-cp311-cp311-win_amd64.whl", hash = "sha256:134da1eca9ec0ae528110ccc9e48041e0828d79f24121a1a146161103c76e686"},
+    {file = "MarkupSafe-2.1.3-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:f698de3fd0c4e6972b92290a45bd9b1536bffe8c6759c62471efaa8acb4c37bc"},
+    {file = "MarkupSafe-2.1.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:aa57bd9cf8ae831a362185ee444e15a93ecb2e344c8e52e4d721ea3ab6ef1823"},
+    {file = "MarkupSafe-2.1.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ffcc3f7c66b5f5b7931a5aa68fc9cecc51e685ef90282f4a82f0f5e9b704ad11"},
+    {file = "MarkupSafe-2.1.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:47d4f1c5f80fc62fdd7777d0d40a2e9dda0a05883ab11374334f6c4de38adffd"},
+    {file = "MarkupSafe-2.1.3-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:1f67c7038d560d92149c060157d623c542173016c4babc0c1913cca0564b9939"},
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+    {file = "MarkupSafe-2.1.3-cp312-cp312-win32.whl", hash = "sha256:715d3562f79d540f251b99ebd6d8baa547118974341db04f5ad06d5ea3eb8007"},
+    {file = "MarkupSafe-2.1.3-cp312-cp312-win_amd64.whl", hash = "sha256:1b8dd8c3fd14349433c79fa8abeb573a55fc0fdd769133baac1f5e07abf54aeb"},
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     {file = "MarkupSafe-2.1.3-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:cb0932dc158471523c9637e807d9bfb93e06a95cbf010f1a38b98623b929ef2b"},
     {file = "MarkupSafe-2.1.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9402b03f1a1b4dc4c19845e5c749e3ab82d5078d16a2a4c2cd2df62d57bb0707"},
@@ -1685,13 +1690,13 @@ test = ["coverage[toml]", "pymdown-extensions", "pytest", "pytest-cov"]
 
 [[package]]
 name = "mkdocs-macros-plugin"
-version = "1.0.4"
+version = "1.0.5"
 description = "Unleash the power of MkDocs with macros and variables"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mkdocs-macros-plugin-1.0.4.tar.gz", hash = "sha256:fc601f142b89cf98743b6b3608d5f93f24daf69b88cfa2320d503c83723c3c6d"},
-    {file = "mkdocs_macros_plugin-1.0.4-py3-none-any.whl", hash = "sha256:c8169443d17212e32df5ad68b562d901acc936d6e87f6b41139dcf13d6659890"},
+    {file = "mkdocs-macros-plugin-1.0.5.tar.gz", hash = "sha256:fe348d75f01c911f362b6d998c57b3d85b505876dde69db924f2c512c395c328"},
+    {file = "mkdocs_macros_plugin-1.0.5-py3-none-any.whl", hash = "sha256:f60e26f711f5a830ddf1e7980865bf5c0f1180db56109803cdd280073c1a050a"},
 ]
 
 [package.dependencies]
@@ -1706,13 +1711,13 @@ test = ["mkdocs-include-markdown-plugin", "mkdocs-macros-test", "mkdocs-material
 
 [[package]]
 name = "mkdocs-material"
-version = "9.4.5"
+version = "9.4.10"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mkdocs_material-9.4.5-py3-none-any.whl", hash = "sha256:0922e3e34d95dbf3f0c84fc817a233e1cbd5874830c6fd821d525ba90e0ce077"},
-    {file = "mkdocs_material-9.4.5.tar.gz", hash = "sha256:efaa52843a8c64b99bcf5a97cf4ba57d410424828e3087b13c9b3954e8adb5ff"},
+    {file = "mkdocs_material-9.4.10-py3-none-any.whl", hash = "sha256:207c4ebc07faebb220437d2c626edb0c9760c82ccfc484500bd3eb30dfce988c"},
+    {file = "mkdocs_material-9.4.10.tar.gz", hash = "sha256:421adedaeaa461dcaf55b8d406673934ade3d4f05ed9819e4cc7b4ee1d646a62"},
 ]
 
 [package.dependencies]
@@ -1721,7 +1726,7 @@ colorama = ">=0.4,<1.0"
 jinja2 = ">=3.0,<4.0"
 markdown = ">=3.2,<4.0"
 mkdocs = ">=1.5.3,<2.0"
-mkdocs-material-extensions = ">=1.2,<2.0"
+mkdocs-material-extensions = ">=1.3,<2.0"
 paginate = ">=0.5,<1.0"
 pygments = ">=2.16,<3.0"
 pymdown-extensions = ">=10.2,<11.0"
@@ -1735,13 +1740,13 @@ recommended = ["mkdocs-minify-plugin (>=0.7,<1.0)", "mkdocs-redirects (>=1.2,<2.
 
 [[package]]
 name = "mkdocs-material-extensions"
-version = "1.2"
+version = "1.3"
 description = "Extension pack for Python Markdown and MkDocs Material."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "mkdocs_material_extensions-1.2-py3-none-any.whl", hash = "sha256:c767bd6d6305f6420a50f0b541b0c9966d52068839af97029be14443849fb8a1"},
-    {file = "mkdocs_material_extensions-1.2.tar.gz", hash = "sha256:27e2d1ed2d031426a6e10d5ea06989d67e90bb02acd588bc5673106b5ee5eedf"},
+    {file = "mkdocs_material_extensions-1.3-py3-none-any.whl", hash = "sha256:0297cc48ba68a9fdd1ef3780a3b41b534b0d0df1d1181a44676fda5f464eeadc"},
+    {file = "mkdocs_material_extensions-1.3.tar.gz", hash = "sha256:f0446091503acb110a7cab9349cbc90eeac51b58d1caa92a704a81ca1e24ddbd"},
 ]
 
 [[package]]
@@ -1808,13 +1813,13 @@ files = [
 
 [[package]]
 name = "nbclient"
-version = "0.8.0"
+version = "0.9.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1830,13 +1835,13 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
 [[package]]
 name = "nbconvert"
-version = "7.9.2"
+version = "7.11.0"
 description = "Converting Jupyter Notebooks"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "nbconvert-7.11.0-py3-none-any.whl", hash = "sha256:d1d417b7f34a4e38887f8da5bdfd12372adf3b80f995d57556cb0972c68909fe"},
+    {file = "nbconvert-7.11.0.tar.gz", hash = "sha256:abedc01cf543177ffde0bfc2a69726d5a478f6af10a332fc1bf29fcb4f0cf000"},
 ]
 
 [package.dependencies]
@@ -1863,7 +1868,7 @@ docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sp
 qtpdf = ["nbconvert[qtpng]"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
-test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest", "pytest-dependency"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest"]
 webpdf = ["playwright"]
 
 [[package]]
@@ -2199,13 +2204,13 @@ files = [
 
 [[package]]
 name = "plac"
-version = "1.4.0"
+version = "1.4.1"
 description = "The smartest command line arguments parser in the world"
 optional = false
 python-versions = "*"
 files = [
-    {file = "plac-1.4.0-py2.py3-none-any.whl", hash = "sha256:6a108d343d61d2b8e770eddd6232dde834012bc005734a688547c482ff65b21a"},
-    {file = "plac-1.4.0.tar.gz", hash = "sha256:334864447ab7c43d2a0700d9387f30cff4843a67c02e65b29854705922b43357"},
+    {file = "plac-1.4.1-py2.py3-none-any.whl", hash = "sha256:5b02d38cfb07c6b95d9803dfdd108a618fdb4691c1759b9156bfb34e566d28c4"},
+    {file = "plac-1.4.1.tar.gz", hash = "sha256:8276d038466f22210ca4f7fa0b270473bea2ec85fff495de179f56934372d5fa"},
 ]
 
 [[package]]
@@ -2258,13 +2263,13 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.39"
+version = "3.0.41"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "prompt_toolkit-3.0.39-py3-none-any.whl", hash = "sha256:9dffbe1d8acf91e3de75f3b544e4842382fc06c6babe903ac9acb74dc6e08d88"},
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+    {file = "prompt_toolkit-3.0.41.tar.gz", hash = "sha256:941367d97fc815548822aa26c2a269fdc4eb21e9ec05fc5d447cf09bad5d75f0"},
 ]
 
 [package.dependencies]
@@ -2272,25 +2277,27 @@ wcwidth = "*"
 
 [[package]]
 name = "psutil"
-version = "5.9.5"
+version = "5.9.6"
 description = "Cross-platform lib for process and system monitoring in Python."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
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+    {file = "psutil-5.9.6-cp37-abi3-win32.whl", hash = "sha256:a6f01f03bf1843280f4ad16f4bde26b817847b4c1a0db59bf6419807bc5ce05c"},
+    {file = "psutil-5.9.6-cp37-abi3-win_amd64.whl", hash = "sha256:6e5fb8dc711a514da83098bc5234264e551ad980cec5f85dabf4d38ed6f15e9a"},
+    {file = "psutil-5.9.6-cp38-abi3-macosx_11_0_arm64.whl", hash = "sha256:daecbcbd29b289aac14ece28eca6a3e60aa361754cf6da3dfb20d4d32b6c7f57"},
+    {file = "psutil-5.9.6.tar.gz", hash = "sha256:e4b92ddcd7dd4cdd3f900180ea1e104932c7bce234fb88976e2a3b296441225a"},
 ]
 
 [package.extras]
@@ -2404,17 +2411,18 @@ urllib3 = ">=1.26.0"
 
 [[package]]
 name = "pygments"
-version = "2.16.1"
+version = "2.17.1"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Pygments-2.16.1-py3-none-any.whl", hash = "sha256:13fc09fa63bc8d8671a6d247e1eb303c4b343eaee81d861f3404db2935653692"},
-    {file = "Pygments-2.16.1.tar.gz", hash = "sha256:1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29"},
+    {file = "pygments-2.17.1-py3-none-any.whl", hash = "sha256:1b37f1b1e1bff2af52ecaf28cc601e2ef7077000b227a0675da25aef85784bc4"},
+    {file = "pygments-2.17.1.tar.gz", hash = "sha256:e45a0e74bf9c530f564ca81b8952343be986a29f6afe7f5ad95c5f06b7bdf5e8"},
 ]
 
 [package.extras]
 plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pyjwt"
@@ -2438,13 +2446,13 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.3"
+version = "10.4"
 description = "Extension pack for Python Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pymdown_extensions-10.3-py3-none-any.whl", hash = "sha256:77a82c621c58a83efc49a389159181d570e370fff9f810d3a4766a75fc678b66"},
-    {file = "pymdown_extensions-10.3.tar.gz", hash = "sha256:94a0d8a03246712b64698af223848fd80aaf1ae4c4be29c8c61939b0467b5722"},
+    {file = "pymdown_extensions-10.4-py3-none-any.whl", hash = "sha256:cfc28d6a09d19448bcbf8eee3ce098c7d17ff99f7bd3069db4819af181212037"},
+    {file = "pymdown_extensions-10.4.tar.gz", hash = "sha256:bc46f11749ecd4d6b71cf62396104b4a200bad3498cb0f5dad1b8502fe461a35"},
 ]
 
 [package.dependencies]
@@ -2522,13 +2530,13 @@ files = [
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.3"
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 python-versions = ">=3.8"
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 [[package]]
@@ -3220,18 +3238,19 @@ all = ["jinja2", "packaging", "pandas", "pygithub", "pyyaml", "requests", "reret
 
 [[package]]
 name = "snakemake"
-version = "7.32.4"
+version = "7.31.1"
 description = "Workflow management system to create reproducible and scalable data analyses"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 appdirs = "*"
 configargparse = "*"
-connection_pool = ">=0.0.3"
+connection-pool = ">=0.0.3"
 datrie = "*"
 docutils = "*"
 gitpython = "*"
@@ -3245,7 +3264,7 @@ pulp = ">=2.0"
 pyyaml = "*"
 requests = "*"
 reretry = "*"
-smart_open = ">=3.0"
+smart-open = ">=3.0"
 stopit = "*"
 tabulate = "*"
 throttler = "*"
@@ -3547,18 +3566,18 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.11.2"
+version = "5.13.0"
 description = "Traitlets Python configuration system"
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 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
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+test = ["argcomplete (>=3.0.3)", "mypy (>=1.6.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "twine"
@@ -3618,18 +3637,17 @@ files = [
 
 [[package]]
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+version = "2.1.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
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+python-versions = ">=3.8"
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 [package.extras]
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-secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
@@ -3649,13 +3667,13 @@ test = ["coverage", "flake8 (>=3.7)", "mypy", "pretend", "pytest"]
 
 [[package]]
 name = "virtualenv"
-version = "20.24.5"
+version = "20.24.6"
 description = "Virtual Python Environment builder"
 optional = true
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 ]
 
 [[package]]
@@ -3882,4 +3895,4 @@ test = ["black", "flake8", "flake8-docstrings", "isort", "pytest", "pytest-cov"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<4.0"
-content-hash = "1b90d27e49ef1fdf589a4f9f37b30c8e8a9e0fbc0617553ac1ad6ecebd638270"
+content-hash = "d46945486370cb26733a9c4da3b6862ba8ab94011a8ffeaa2000c480e670a8da"
diff --git a/pyproject.toml b/pyproject.toml
index 24947bd..976c403 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ click = "^8.1.3"
 snakedeploy = "^0.8.2"
 peppy = "^0.35.4"
 panoptes-ui = "^0.2.0"
-snakemake = "^7.18.2"
+snakemake = "7.31.1"
 mkdocs-jupyter = "^0.24.2"
 mkdocs-macros-plugin = "^1.0.4"
 setuptools = "^65.5.1"