From c7e484d538068f26d750b2e66782512a99bcabed Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Wed, 4 Dec 2024 10:45:16 -0700
Subject: [PATCH] fix

---
 conda-requirements.txt |    2 +-
 poetry.lock            | 1544 ++++++++++++++++++++++++----------------
 2 files changed, 925 insertions(+), 621 deletions(-)

diff --git a/conda-requirements.txt b/conda-requirements.txt
index dfa2abb..d64e3de 100644
--- a/conda-requirements.txt
+++ b/conda-requirements.txt
@@ -1,3 +1,3 @@
 # Setup python version and poetry
 python=3.9
-poetry=1.0.5
+poetry=1.8.3
diff --git a/poetry.lock b/poetry.lock
index 9315ed4..5e53de1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,33 +1,62 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+
 [[package]]
-category = "dev"
-description = "Atomic file writes."
-marker = "sys_platform == \"win32\""
 name = "atomicwrites"
+version = "1.4.1"
+description = "Atomic file writes."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.4.1"
+files = [
+    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
 
 [[package]]
-category = "main"
-description = "Classes Without Boilerplate"
 name = "attrs"
+version = "19.3.0"
+description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "19.3.0"
+files = [
+    {file = "attrs-19.3.0-py2.py3-none-any.whl", hash = "sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c"},
+    {file = "attrs-19.3.0.tar.gz", hash = "sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"},
+]
 
 [package.extras]
-azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
-dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
+azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-azurepipelines", "six", "zope.interface"]
+dev = ["coverage", "hypothesis", "pre-commit", "pympler", "pytest (>=4.3.0)", "six", "sphinx", "zope.interface"]
 docs = ["sphinx", "zope.interface"]
 tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
 
 [[package]]
-category = "dev"
-description = "The uncompromising code formatter."
 name = "black"
+version = "23.12.1"
+description = "The uncompromising code formatter."
 optional = false
-python-versions = ">=3.7"
-version = "23.1.0"
+python-versions = ">=3.8"
+files = [
+    {file = "black-23.12.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e0aaf6041986767a5e0ce663c7a2f0e9eaf21e6ff87a5f95cbf3675bfd4c41d2"},
+    {file = "black-23.12.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c88b3711d12905b74206227109272673edce0cb29f27e1385f33b0163c414bba"},
+    {file = "black-23.12.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a920b569dc6b3472513ba6ddea21f440d4b4c699494d2e972a1753cdc25df7b0"},
+    {file = "black-23.12.1-cp310-cp310-win_amd64.whl", hash = "sha256:3fa4be75ef2a6b96ea8d92b1587dd8cb3a35c7e3d51f0738ced0781c3aa3a5a3"},
+    {file = "black-23.12.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:8d4df77958a622f9b5a4c96edb4b8c0034f8434032ab11077ec6c56ae9f384ba"},
+    {file = "black-23.12.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:602cfb1196dc692424c70b6507593a2b29aac0547c1be9a1d1365f0d964c353b"},
+    {file = "black-23.12.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9c4352800f14be5b4864016882cdba10755bd50805c95f728011bcb47a4afd59"},
+    {file = "black-23.12.1-cp311-cp311-win_amd64.whl", hash = "sha256:0808494f2b2df923ffc5723ed3c7b096bd76341f6213989759287611e9837d50"},
+    {file = "black-23.12.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:25e57fd232a6d6ff3f4478a6fd0580838e47c93c83eaf1ccc92d4faf27112c4e"},
+    {file = "black-23.12.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:2d9e13db441c509a3763a7a3d9a49ccc1b4e974a47be4e08ade2a228876500ec"},
+    {file = "black-23.12.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6d1bd9c210f8b109b1762ec9fd36592fdd528485aadb3f5849b2740ef17e674e"},
+    {file = "black-23.12.1-cp312-cp312-win_amd64.whl", hash = "sha256:ae76c22bde5cbb6bfd211ec343ded2163bba7883c7bc77f6b756a1049436fbb9"},
+    {file = "black-23.12.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:1fa88a0f74e50e4487477bc0bb900c6781dbddfdfa32691e780bf854c3b4a47f"},
+    {file = "black-23.12.1-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:a4d6a9668e45ad99d2f8ec70d5c8c04ef4f32f648ef39048d010b0689832ec6d"},
+    {file = "black-23.12.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b18fb2ae6c4bb63eebe5be6bd869ba2f14fd0259bda7d18a46b764d8fb86298a"},
+    {file = "black-23.12.1-cp38-cp38-win_amd64.whl", hash = "sha256:c04b6d9d20e9c13f43eee8ea87d44156b8505ca8a3c878773f68b4e4812a421e"},
+    {file = "black-23.12.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:3e1b38b3135fd4c025c28c55ddfc236b05af657828a8a6abe5deec419a0b7055"},
+    {file = "black-23.12.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:4f0031eaa7b921db76decd73636ef3a12c942ed367d8c3841a0739412b260a54"},
+    {file = "black-23.12.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:97e56155c6b737854e60a9ab1c598ff2533d57e7506d97af5481141671abf3ea"},
+    {file = "black-23.12.1-cp39-cp39-win_amd64.whl", hash = "sha256:dd15245c8b68fe2b6bd0f32c1556509d11bb33aec9b5d0866dd8e2ed3dba09c2"},
+    {file = "black-23.12.1-py3-none-any.whl", hash = "sha256:78baad24af0f033958cad29731e27363183e140962595def56423e626f4bee3e"},
+    {file = "black-23.12.1.tar.gz", hash = "sha256:4ce3ef14ebe8d9509188014d96af1c456a910d5b5cbf434a09fef7e024b3d0d5"},
+]
 
 [package.dependencies]
 click = ">=8.0.0"
@@ -35,522 +64,658 @@ mypy-extensions = ">=0.4.3"
 packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
-
-[package.dependencies.tomli]
-python = "<3.11"
-version = ">=1.1.0"
-
-[package.dependencies.typing-extensions]
-python = "<3.10"
-version = ">=3.10.0.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
+d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
-category = "main"
-description = "The AWS SDK for Python"
 name = "boto3"
+version = "1.35.74"
+description = "The AWS SDK for Python"
 optional = false
-python-versions = ">= 3.7"
-version = "1.26.88"
+python-versions = ">=3.8"
+files = [
+    {file = "boto3-1.35.74-py3-none-any.whl", hash = "sha256:dab5bddbbe57dc707b6f6a1f25dc2823b8e234b6fe99fafef7fc406ab73031b9"},
+    {file = "boto3-1.35.74.tar.gz", hash = "sha256:88370c6845ba71a4dae7f6b357099df29b3965da584be040c8e72c9902bc9492"},
+]
 
 [package.dependencies]
-botocore = ">=1.29.88,<1.30.0"
+botocore = ">=1.35.74,<1.36.0"
 jmespath = ">=0.7.1,<2.0.0"
-s3transfer = ">=0.6.0,<0.7.0"
+s3transfer = ">=0.10.0,<0.11.0"
 
 [package.extras]
-crt = ["botocore (>=1.21.0,<2.0a0)"]
+crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
-category = "main"
-description = "Type annotations for boto3 1.26.88 generated with mypy-boto3-builder 7.12.5"
 name = "boto3-stubs"
+version = "1.35.74"
+description = "Type annotations for boto3 1.35.74 generated with mypy-boto3-builder 8.5.0"
 optional = false
-python-versions = ">=3.7"
-version = "1.26.88"
+python-versions = ">=3.8"
+files = [
+    {file = "boto3_stubs-1.35.74-py3-none-any.whl", hash = "sha256:6b24d9b327bd33985d8c9b7a9a47af00ce60e19b93bf50c3876ebbe26127d332"},
+    {file = "boto3_stubs-1.35.74.tar.gz", hash = "sha256:f11dce081d1365d41e13c16cb5f8620f7b86d8c4093e801d10d96229174a7607"},
+]
 
 [package.dependencies]
 botocore-stubs = "*"
+mypy-boto3-batch = {version = ">=1.35.0,<1.36.0", optional = true, markers = "extra == \"batch\""}
+mypy-boto3-logs = {version = ">=1.35.0,<1.36.0", optional = true, markers = "extra == \"logs\""}
 types-s3transfer = "*"
-typing-extensions = ">=4.1.0"
-
-[package.dependencies.mypy-boto3-batch]
-optional = true
-version = ">=1.26.0,<1.27.0"
-
-[package.dependencies.mypy-boto3-logs]
-optional = true
-version = ">=1.26.0,<1.27.0"
+typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.12\""}
 
 [package.extras]
-accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.26.0,<1.27.0)"]
-account = ["mypy-boto3-account (>=1.26.0,<1.27.0)"]
-acm = ["mypy-boto3-acm (>=1.26.0,<1.27.0)"]
-acm-pca = ["mypy-boto3-acm-pca (>=1.26.0,<1.27.0)"]
-alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.26.0,<1.27.0)"]
-all = ["mypy-boto3-accessanalyzer (>=1.26.0,<1.27.0)", "mypy-boto3-account (>=1.26.0,<1.27.0)", "mypy-boto3-acm (>=1.26.0,<1.27.0)", "mypy-boto3-acm-pca (>=1.26.0,<1.27.0)", "mypy-boto3-alexaforbusiness (>=1.26.0,<1.27.0)", "mypy-boto3-amp (>=1.26.0,<1.27.0)", "mypy-boto3-amplify (>=1.26.0,<1.27.0)", "mypy-boto3-amplifybackend (>=1.26.0,<1.27.0)", "mypy-boto3-amplifyuibuilder (>=1.26.0,<1.27.0)", "mypy-boto3-apigateway (>=1.26.0,<1.27.0)", "mypy-boto3-apigatewaymanagementapi (>=1.26.0,<1.27.0)", "mypy-boto3-apigatewayv2 (>=1.26.0,<1.27.0)", "mypy-boto3-appconfig (>=1.26.0,<1.27.0)", "mypy-boto3-appconfigdata (>=1.26.0,<1.27.0)", "mypy-boto3-appflow (>=1.26.0,<1.27.0)", "mypy-boto3-appintegrations (>=1.26.0,<1.27.0)", "mypy-boto3-application-autoscaling (>=1.26.0,<1.27.0)", "mypy-boto3-application-insights (>=1.26.0,<1.27.0)", "mypy-boto3-applicationcostprofiler (>=1.26.0,<1.27.0)", "mypy-boto3-appmesh (>=1.26.0,<1.27.0)", "mypy-boto3-apprunner (>=1.26.0,<1.27.0)", "mypy-boto3-appstream (>=1.26.0,<1.27.0)", "mypy-boto3-appsync (>=1.26.0,<1.27.0)", "mypy-boto3-arc-zonal-shift (>=1.26.0,<1.27.0)", "mypy-boto3-athena (>=1.26.0,<1.27.0)", "mypy-boto3-auditmanager (>=1.26.0,<1.27.0)", "mypy-boto3-autoscaling (>=1.26.0,<1.27.0)", "mypy-boto3-autoscaling-plans (>=1.26.0,<1.27.0)", "mypy-boto3-backup (>=1.26.0,<1.27.0)", "mypy-boto3-backup-gateway (>=1.26.0,<1.27.0)", "mypy-boto3-backupstorage (>=1.26.0,<1.27.0)", "mypy-boto3-batch (>=1.26.0,<1.27.0)", "mypy-boto3-billingconductor (>=1.26.0,<1.27.0)", "mypy-boto3-braket (>=1.26.0,<1.27.0)", "mypy-boto3-budgets (>=1.26.0,<1.27.0)", "mypy-boto3-ce (>=1.26.0,<1.27.0)", "mypy-boto3-chime (>=1.26.0,<1.27.0)", "mypy-boto3-chime-sdk-identity (>=1.26.0,<1.27.0)", "mypy-boto3-chime-sdk-media-pipelines (>=1.26.0,<1.27.0)", "mypy-boto3-chime-sdk-meetings (>=1.26.0,<1.27.0)", "mypy-boto3-chime-sdk-messaging (>=1.26.0,<1.27.0)", "mypy-boto3-chime-sdk-voice (>=1.26.0,<1.27.0)", "mypy-boto3-cleanrooms (>=1.26.0,<1.27.0)", "mypy-boto3-cloud9 (>=1.26.0,<1.27.0)", "mypy-boto3-cloudcontrol (>=1.26.0,<1.27.0)", "mypy-boto3-clouddirectory (>=1.26.0,<1.27.0)", "mypy-boto3-cloudformation (>=1.26.0,<1.27.0)", "mypy-boto3-cloudfront (>=1.26.0,<1.27.0)", "mypy-boto3-cloudhsm (>=1.26.0,<1.27.0)", "mypy-boto3-cloudhsmv2 (>=1.26.0,<1.27.0)", "mypy-boto3-cloudsearch (>=1.26.0,<1.27.0)", "mypy-boto3-cloudsearchdomain (>=1.26.0,<1.27.0)", "mypy-boto3-cloudtrail (>=1.26.0,<1.27.0)", "mypy-boto3-cloudtrail-data (>=1.26.0,<1.27.0)", "mypy-boto3-cloudwatch (>=1.26.0,<1.27.0)", "mypy-boto3-codeartifact (>=1.26.0,<1.27.0)", "mypy-boto3-codebuild (>=1.26.0,<1.27.0)", "mypy-boto3-codecatalyst (>=1.26.0,<1.27.0)", "mypy-boto3-codecommit (>=1.26.0,<1.27.0)", "mypy-boto3-codedeploy (>=1.26.0,<1.27.0)", "mypy-boto3-codeguru-reviewer (>=1.26.0,<1.27.0)", "mypy-boto3-codeguruprofiler (>=1.26.0,<1.27.0)", "mypy-boto3-codepipeline (>=1.26.0,<1.27.0)", "mypy-boto3-codestar (>=1.26.0,<1.27.0)", "mypy-boto3-codestar-connections (>=1.26.0,<1.27.0)", "mypy-boto3-codestar-notifications (>=1.26.0,<1.27.0)", "mypy-boto3-cognito-identity (>=1.26.0,<1.27.0)", "mypy-boto3-cognito-idp (>=1.26.0,<1.27.0)", "mypy-boto3-cognito-sync (>=1.26.0,<1.27.0)", "mypy-boto3-comprehend (>=1.26.0,<1.27.0)", "mypy-boto3-comprehendmedical (>=1.26.0,<1.27.0)", "mypy-boto3-compute-optimizer (>=1.26.0,<1.27.0)", "mypy-boto3-config (>=1.26.0,<1.27.0)", "mypy-boto3-connect (>=1.26.0,<1.27.0)", "mypy-boto3-connect-contact-lens (>=1.26.0,<1.27.0)", "mypy-boto3-connectcampaigns (>=1.26.0,<1.27.0)", "mypy-boto3-connectcases (>=1.26.0,<1.27.0)", "mypy-boto3-connectparticipant (>=1.26.0,<1.27.0)", "mypy-boto3-controltower (>=1.26.0,<1.27.0)", "mypy-boto3-cur (>=1.26.0,<1.27.0)", "mypy-boto3-customer-profiles (>=1.26.0,<1.27.0)", "mypy-boto3-databrew (>=1.26.0,<1.27.0)", "mypy-boto3-dataexchange (>=1.26.0,<1.27.0)", "mypy-boto3-datapipeline (>=1.26.0,<1.27.0)", "mypy-boto3-datasync (>=1.26.0,<1.27.0)", 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+]
 
 [package.dependencies]
-[package.dependencies.tomli]
-optional = true
-python = "<=3.11.0a6"
-version = "*"
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
 toml = ["tomli"]
 
 [[package]]
-category = "main"
-description = "Effortless argument parser"
 name = "defopt"
+version = "6.4.0"
+description = "Effortless argument parser"
 optional = false
 python-versions = ">=3.5"
-version = "6.4.0"
+files = [
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+]
 
 [package.dependencies]
-colorama = ">=0.3.4"
+colorama = {version = ">=0.3.4", markers = "sys_platform == \"win32\""}
 docutils = ">=0.12"
 sphinxcontrib-napoleon = ">=0.7.0"
 
-[package.dependencies.pkgutil_resolve_name]
-python = "<3.9"
-version = "*"
-
-[package.dependencies.typing_extensions]
-python = "<3.9"
-version = ">=3.7.4"
-
 [package.extras]
 docs = ["sphinx (>=4.4)"]
 
 [[package]]
-category = "main"
-description = "Docutils -- Python Documentation Utilities"
 name = "docutils"
+version = "0.21.2"
+description = "Docutils -- Python Documentation Utilities"
 optional = false
-python-versions = ">=3.7"
-version = "0.19"
+python-versions = ">=3.9"
+files = [
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+]
 
 [[package]]
-category = "main"
-description = "Python bioinformatics and genomics library"
 name = "fgpyo"
+version = "0.0.6"
+description = "Python bioinformatics and genomics library"
 optional = false
 python-versions = ">=3.7.0,<4.0"
-version = "0.0.6"
+files = [
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+]
 
 [package.dependencies]
 attrs = ">=19.3.0"
 pysam = ">=0.20.0"
 
 [package.extras]
-docs = ["sphinx (4.3.1)"]
+docs = ["sphinx (==4.3.1)"]
 
 [[package]]
-category = "dev"
-description = "the modular source code checker: pep8 pyflakes and co"
 name = "flake8"
+version = "3.9.2"
+description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-version = "3.9.2"
+files = [
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+]
 
 [package.dependencies]
 mccabe = ">=0.6.0,<0.7.0"
@@ -558,36 +723,60 @@ pycodestyle = ">=2.7.0,<2.8.0"
 pyflakes = ">=2.3.0,<2.4.0"
 
 [[package]]
-category = "main"
-description = "JSON Matching Expressions"
 name = "jmespath"
+version = "1.0.1"
+description = "JSON Matching Expressions"
 optional = false
 python-versions = ">=3.7"
-version = "1.0.1"
+files = [
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+    {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"},
+]
 
 [[package]]
-category = "dev"
-description = "McCabe checker, plugin for flake8"
 name = "mccabe"
+version = "0.6.1"
+description = "McCabe checker, plugin for flake8"
 optional = false
 python-versions = "*"
-version = "0.6.1"
+files = [
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+]
 
 [[package]]
-category = "dev"
-description = "More routines for operating on iterables, beyond itertools"
 name = "more-itertools"
+version = "10.5.0"
+description = "More routines for operating on iterables, beyond itertools"
 optional = false
-python-versions = ">=3.7"
-version = "9.1.0"
+python-versions = ">=3.8"
+files = [
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+]
 
 [[package]]
-category = "dev"
-description = "Optional static typing for Python"
 name = "mypy"
+version = "0.770"
+description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.5"
-version = "0.770"
+files = [
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+    {file = "mypy-0.770-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:7ec45a70d40ede1ec7ad7f95b3c94c9cf4c186a32f6bacb1795b60abd2f9ef27"},
+    {file = "mypy-0.770-cp38-cp38-win_amd64.whl", hash = "sha256:f91c7ae919bbc3f96cd5e5b2e786b2b108343d1d7972ea130f7de27fdd547cf3"},
+    {file = "mypy-0.770-py3-none-any.whl", hash = "sha256:3b1fc683fb204c6b4403a1ef23f0b1fac8e4477091585e0c8c54cbdf7d7bb164"},
+    {file = "mypy-0.770.tar.gz", hash = "sha256:8a627507ef9b307b46a1fea9513d5c98680ba09591253082b4c48697ba05a4ae"},
+]
 
 [package.dependencies]
 mypy-extensions = ">=0.4.3,<0.5.0"
@@ -598,146 +787,203 @@ typing-extensions = ">=3.7.4"
 dmypy = ["psutil (>=4.0)"]
 
 [[package]]
-category = "main"
-description = "Type annotations for boto3.Batch 1.26.34 service generated with mypy-boto3-builder 7.12.0"
 name = "mypy-boto3-batch"
+version = "1.35.57"
+description = "Type annotations for boto3.Batch 1.35.57 service generated with mypy-boto3-builder 8.2.1"
 optional = false
-python-versions = ">=3.7"
-version = "1.26.34"
+python-versions = ">=3.8"
+files = [
+    {file = "mypy_boto3_batch-1.35.57-py3-none-any.whl", hash = "sha256:186a0a22f675cff06c3ae8eee563b9d93d56a992513287d1f92a18bb20f11b24"},
+    {file = "mypy_boto3_batch-1.35.57.tar.gz", hash = "sha256:d6d5890fbf348a8b3086d742075113951c04544c4225bc23b4b703835c7f1c6d"},
+]
 
 [package.dependencies]
-typing-extensions = ">=4.1.0"
+typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.12\""}
 
 [[package]]
-category = "main"
-description = "Type annotations for boto3.CloudWatchLogs 1.26.53 service generated with mypy-boto3-builder 7.12.3"
 name = "mypy-boto3-logs"
+version = "1.35.72"
+description = "Type annotations for boto3 CloudWatchLogs 1.35.72 service generated with mypy-boto3-builder 8.5.0"
 optional = false
-python-versions = ">=3.7"
-version = "1.26.53"
+python-versions = ">=3.8"
+files = [
+    {file = "mypy_boto3_logs-1.35.72-py3-none-any.whl", hash = "sha256:026359f73dc2b428e53b8230a503c4a23b4c1a5b0383e49179ad937a75339269"},
+    {file = "mypy_boto3_logs-1.35.72.tar.gz", hash = "sha256:6088ba40021d82251067468235a43c112a6a941071fb1c521d00799b2a85e04a"},
+]
 
 [package.dependencies]
-typing-extensions = ">=4.1.0"
+typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.12\""}
 
 [[package]]
-category = "dev"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
 name = "mypy-extensions"
+version = "0.4.4"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
 optional = false
 python-versions = ">=2.7"
-version = "0.4.4"
+files = [
+    {file = "mypy_extensions-0.4.4.tar.gz", hash = "sha256:c8b707883a96efe9b4bb3aaf0dcc07e7e217d7d8368eec4db4049ee9e142f4fd"},
+]
 
 [[package]]
-category = "main"
-description = "Generate Random Names for anything"
 name = "namegenerator"
+version = "1.0.6"
+description = "Generate Random Names for anything"
 optional = false
 python-versions = "*"
-version = "1.0.6"
+files = [
+    {file = "namegenerator-1.0.6.tar.gz", hash = "sha256:144759c62d771e5b589514a0aa332d0b967818c0a24b7824e48a905357c58bfa"},
+]
 
 [[package]]
-category = "dev"
-description = "Core utilities for Python packages"
 name = "packaging"
+version = "24.2"
+description = "Core utilities for Python packages"
 optional = false
-python-versions = ">=3.7"
-version = "23.0"
+python-versions = ">=3.8"
+files = [
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+]
 
 [[package]]
-category = "dev"
-description = "Utility library for gitignore style pattern matching of file paths."
 name = "pathspec"
+version = "0.12.1"
+description = "Utility library for gitignore style pattern matching of file paths."
 optional = false
-python-versions = ">=3.7"
-version = "0.11.0"
-
-[[package]]
-category = "main"
-description = "Resolve a name to an object."
-marker = "python_version < \"3.9\""
-name = "pkgutil-resolve-name"
-optional = false
-python-versions = ">=3.6"
-version = "1.3.10"
+python-versions = ">=3.8"
+files = [
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+]
 
 [[package]]
-category = "dev"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 name = "platformdirs"
+version = "4.3.6"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
-python-versions = ">=3.7"
-version = "3.1.0"
+python-versions = ">=3.8"
+files = [
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+]
 
 [package.extras]
-docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.22,<1.23.4 || >1.23.4)", "sphinx (>=6.1.3)"]
-test = ["appdirs (1.4.4)", "covdefaults (>=2.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest (>=7.2.1)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
-category = "dev"
-description = "plugin and hook calling mechanisms for python"
 name = "pluggy"
+version = "0.13.1"
+description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.13.1"
+files = [
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+    {file = "pluggy-0.13.1.tar.gz", hash = "sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0"},
+]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 
 [[package]]
-category = "main"
-description = "A collection of helpful Python tools!"
 name = "pockets"
+version = "0.9.1"
+description = "A collection of helpful Python tools!"
 optional = false
 python-versions = "*"
-version = "0.9.1"
+files = [
+    {file = "pockets-0.9.1-py2.py3-none-any.whl", hash = "sha256:68597934193c08a08eb2bf6a1d85593f627c22f9b065cc727a4f03f669d96d86"},
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+]
 
 [package.dependencies]
 six = ">=1.5.2"
 
 [[package]]
-category = "dev"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
 name = "py"
+version = "1.11.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "1.11.0"
+files = [
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+]
 
 [[package]]
-category = "dev"
-description = "Python style guide checker"
 name = "pycodestyle"
+version = "2.7.0"
+description = "Python style guide checker"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.7.0"
+files = [
+    {file = "pycodestyle-2.7.0-py2.py3-none-any.whl", hash = "sha256:514f76d918fcc0b55c6680472f0a37970994e07bbb80725808c17089be302068"},
+    {file = "pycodestyle-2.7.0.tar.gz", hash = "sha256:c389c1d06bf7904078ca03399a4816f974a1d590090fecea0c63ec26ebaf1cef"},
+]
 
 [[package]]
-category = "dev"
-description = "passive checker of Python programs"
 name = "pyflakes"
+version = "2.3.1"
+description = "passive checker of Python programs"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.3.1"
+files = [
+    {file = "pyflakes-2.3.1-py2.py3-none-any.whl", hash = "sha256:7893783d01b8a89811dd72d7dfd4d84ff098e5eed95cfa8905b22bbffe52efc3"},
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+]
 
 [[package]]
-category = "main"
-description = "pysam"
 name = "pysam"
+version = "0.22.1"
+description = "Package for reading, manipulating, and writing genomic data"
 optional = false
-python-versions = "*"
-version = "0.20.0"
+python-versions = ">=3.6"
+files = [
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+]
 
 [[package]]
-category = "dev"
-description = "pytest: simple powerful testing with Python"
 name = "pytest"
+version = "5.4.3"
+description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.5"
-version = "5.4.3"
+files = [
+    {file = "pytest-5.4.3-py3-none-any.whl", hash = "sha256:5c0db86b698e8f170ba4582a492248919255fcd4c79b1ee64ace34301fb589a1"},
+    {file = "pytest-5.4.3.tar.gz", hash = "sha256:7979331bfcba207414f5e1263b5a0f8f521d0f457318836a7355531ed1a4c7d8"},
+]
 
 [package.dependencies]
-atomicwrites = ">=1.0"
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=17.4.0"
-colorama = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
 more-itertools = ">=4.0.0"
 packaging = "*"
 pluggy = ">=0.12,<1.0"
@@ -745,184 +991,242 @@ py = ">=1.5.0"
 wcwidth = "*"
 
 [package.extras]
-checkqa-mypy = ["mypy (v0.761)"]
+checkqa-mypy = ["mypy (==v0.761)"]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
-category = "dev"
-description = "Pytest plugin for measuring coverage."
 name = "pytest-cov"
+version = "6.0.0"
+description = "Pytest plugin for measuring coverage."
 optional = false
-python-versions = ">=3.6"
-version = "4.0.0"
+python-versions = ">=3.9"
+files = [
+    {file = "pytest-cov-6.0.0.tar.gz", hash = "sha256:fde0b595ca248bb8e2d76f020b465f3b107c9632e6a1d1705f17834c89dcadc0"},
+    {file = "pytest_cov-6.0.0-py3-none-any.whl", hash = "sha256:eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35"},
+]
 
 [package.dependencies]
+coverage = {version = ">=7.5", extras = ["toml"]}
 pytest = ">=4.6"
 
-[package.dependencies.coverage]
-extras = ["toml"]
-version = ">=5.2.1"
-
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 
 [[package]]
-category = "main"
-description = "Extensions to the standard Python datetime module"
 name = "python-dateutil"
+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"
-version = "2.8.2"
+files = [
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+    {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
+]
 
 [package.dependencies]
 six = ">=1.5"
 
 [[package]]
-category = "main"
-description = "An Amazon S3 Transfer Manager"
 name = "s3transfer"
+version = "0.10.4"
+description = "An Amazon S3 Transfer Manager"
 optional = false
-python-versions = ">= 3.7"
-version = "0.6.0"
+python-versions = ">=3.8"
+files = [
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+    {file = "s3transfer-0.10.4.tar.gz", hash = "sha256:29edc09801743c21eb5ecbc617a152df41d3c287f67b615f73e5f750583666a7"},
+]
 
 [package.dependencies]
-botocore = ">=1.12.36,<2.0a.0"
+botocore = ">=1.33.2,<2.0a.0"
 
 [package.extras]
-crt = ["botocore (>=1.20.29,<2.0a.0)"]
+crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"]
 
 [[package]]
-category = "main"
-description = "Python 2 and 3 compatibility utilities"
 name = "six"
+version = "1.17.0"
+description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "1.16.0"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+files = [
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+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
+]
 
 [[package]]
-category = "main"
-description = "Sphinx \"napoleon\" extension."
 name = "sphinxcontrib-napoleon"
+version = "0.7"
+description = "Sphinx \"napoleon\" extension."
 optional = false
 python-versions = "*"
-version = "0.7"
+files = [
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+]
 
 [package.dependencies]
 pockets = ">=0.3"
 six = ">=1.5.2"
 
 [[package]]
-category = "dev"
-description = "A lil' TOML parser"
-marker = "python_full_version <= \"3.11.0a6\" or python_version < \"3.11\""
 name = "tomli"
+version = "2.2.1"
+description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
-version = "2.0.1"
+python-versions = ">=3.8"
+files = [
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