From 7e142b1c655c6151ad2a805a5f11db6233380f32 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 22 Aug 2023 15:39:39 -0400
Subject: [PATCH 01/35] Up pyyaml version to ^6.0.1 for Mac M1 issue with
 build.

---
 poetry.lock    | 142 +++++++++++++++----------------------------------
 pyproject.toml |   2 +-
 2 files changed, 45 insertions(+), 99 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d7e77523c..1a4b10c74 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "async-timeout"
 version = "4.0.2"
 description = "Timeout context manager for asyncio programs"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -19,7 +18,6 @@ typing-extensions = {version = ">=3.6.5", markers = "python_version < \"3.8\""}
 name = "aws-requests-auth"
 version = "0.4.3"
 description = "AWS signature version 4 signing process for the python requests module"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -34,7 +32,6 @@ requests = ">=0.14.0"
 name = "beautifulsoup4"
 version = "4.12.2"
 description = "Screen-scraping library"
-category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -53,7 +50,6 @@ lxml = ["lxml"]
 name = "boto3"
 version = "1.28.20"
 description = "The AWS SDK for Python"
-category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
@@ -73,7 +69,6 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 name = "boto3-stubs"
 version = "1.18.23"
 description = "Type annotations for boto3 1.18.23, generated by mypy-boto3-builder 5.1.0"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -369,7 +364,6 @@ xray = ["mypy-boto3-xray (>=1.18.18)"]
 name = "botocore"
 version = "1.31.20"
 description = "Low-level, data-driven core of boto 3."
-category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
@@ -389,7 +383,6 @@ crt = ["awscrt (==0.16.26)"]
 name = "botocore-stubs"
 version = "1.21.22"
 description = "Type annotations for botocore 1.21.22, generated by mypy-boto3-builder 5.1.0"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -404,7 +397,6 @@ typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
 name = "certifi"
 version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -416,7 +408,6 @@ files = [
 name = "cffi"
 version = "1.15.1"
 description = "Foreign Function Interface for Python calling C code."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -493,7 +484,6 @@ pycparser = "*"
 name = "charset-normalizer"
 version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -578,7 +568,6 @@ files = [
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -590,7 +579,6 @@ files = [
 name = "coverage"
 version = "7.2.7"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -666,7 +654,6 @@ toml = ["tomli"]
 name = "cryptography"
 version = "41.0.3"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -712,7 +699,6 @@ test-randomorder = ["pytest-randomly"]
 name = "docker"
 version = "4.4.4"
 description = "A Python library for the Docker Engine API."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -734,7 +720,6 @@ tls = ["cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"]
 name = "elasticsearch"
 version = "7.13.4"
 description = "Python client for Elasticsearch"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4"
 files = [
@@ -756,7 +741,6 @@ requests = ["requests (>=2.4.0,<3.0.0)"]
 name = "exceptiongroup"
 version = "1.1.2"
 description = "Backport of PEP 654 (exception groups)"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -771,7 +755,6 @@ test = ["pytest (>=6)"]
 name = "flake8"
 version = "5.0.4"
 description = "the modular source code checker: pep8 pyflakes and co"
-category = "dev"
 optional = false
 python-versions = ">=3.6.1"
 files = [
@@ -789,7 +772,6 @@ pyflakes = ">=2.5.0,<2.6.0"
 name = "flaky"
 version = "3.7.0"
 description = "Plugin for nose or pytest that automatically reruns flaky tests."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -801,7 +783,6 @@ files = [
 name = "gitdb"
 version = "4.0.10"
 description = "Git Object Database"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -816,7 +797,6 @@ smmap = ">=3.0.1,<6"
 name = "gitpython"
 version = "3.1.32"
 description = "GitPython is a Python library used to interact with Git repositories"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -832,7 +812,6 @@ typing-extensions = {version = ">=3.7.4.3", markers = "python_version < \"3.8\""
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -844,7 +823,6 @@ files = [
 name = "importlib-metadata"
 version = "4.2.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -864,7 +842,6 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pep517",
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -876,7 +853,6 @@ files = [
 name = "jmespath"
 version = "1.0.1"
 description = "JSON Matching Expressions"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -888,7 +864,6 @@ files = [
 name = "mccabe"
 version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -900,7 +875,6 @@ files = [
 name = "mirakuru"
 version = "2.5.1"
 description = "Process executor (not only) for tests."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -915,7 +889,6 @@ psutil = {version = ">=4.0.0", markers = "sys_platform != \"cygwin\""}
 name = "opensearch-py"
 version = "2.3.0"
 description = "Python client for OpenSearch"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4"
 files = [
@@ -940,7 +913,6 @@ kerberos = ["requests-kerberos"]
 name = "packaging"
 version = "23.1"
 description = "Core utilities for Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -952,7 +924,6 @@ files = [
 name = "pip-licenses"
 version = "3.5.5"
 description = "Dump the software license list of Python packages installed with pip."
-category = "dev"
 optional = false
 python-versions = "~=3.7"
 files = [
@@ -970,7 +941,6 @@ test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"]
 name = "pluggy"
 version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -989,7 +959,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "port-for"
 version = "0.7.1"
 description = "Utility that helps with local TCP ports management. It can find an unused TCP localhost port and remember the association."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1001,7 +970,6 @@ files = [
 name = "psutil"
 version = "5.9.5"
 description = "Cross-platform lib for process and system monitoring in Python."
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1028,7 +996,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "ptable"
 version = "0.9.2"
 description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1039,7 +1006,6 @@ files = [
 name = "pycodestyle"
 version = "2.9.1"
 description = "Python style guide checker"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1051,7 +1017,6 @@ files = [
 name = "pycparser"
 version = "2.21"
 description = "C parser in Python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1063,7 +1028,6 @@ files = [
 name = "pyflakes"
 version = "2.5.0"
 description = "passive checker of Python programs"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1075,7 +1039,6 @@ files = [
 name = "pyjwt"
 version = "2.8.0"
 description = "JSON Web Token implementation in Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1096,7 +1059,6 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 name = "pyopenssl"
 version = "23.2.0"
 description = "Python wrapper module around the OpenSSL library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1115,7 +1077,6 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"]
 name = "pytest"
 version = "7.4.0"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1139,7 +1100,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 name = "pytest-cov"
 version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1158,7 +1118,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 name = "pytest-mock"
 version = "3.11.1"
 description = "Thin-wrapper around the mock package for easier use with pytest"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1176,7 +1135,6 @@ dev = ["pre-commit", "pytest-asyncio", "tox"]
 name = "pytest-redis"
 version = "2.4.0"
 description = "Redis fixtures and fixture factories for Pytest."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1197,7 +1155,6 @@ tests = ["mock", "pytest-cov", "pytest-xdist"]
 name = "pytest-runner"
 version = "6.0.0"
 description = "Invoke py.test as distutils command with dependency resolution"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1213,7 +1170,6 @@ testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)",
 name = "python-dateutil"
 version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1228,7 +1184,6 @@ six = ">=1.5"
 name = "pytz"
 version = "2023.3"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1240,7 +1195,6 @@ files = [
 name = "pywin32"
 version = "227"
 description = "Python for Window Extensions"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1260,48 +1214,57 @@ files = [
 
 [[package]]
 name = "pyyaml"
-version = "5.4.1"
+version = "6.0.1"
 description = "YAML parser and emitter for Python"
-category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.6"
 files = [
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+    {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673"},
+    {file = "PyYAML-6.0.1-cp311-cp311-win32.whl", hash = "sha256:1635fd110e8d85d55237ab316b5b011de701ea0f29d07611174a1b42f1444741"},
+    {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
+    {file = "PyYAML-6.0.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47"},
+    {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98"},
+    {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c"},
+    {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:afd7e57eddb1a54f0f1a974bc4391af8bcce0b444685d936840f125cf046d5bd"},
+    {file = "PyYAML-6.0.1-cp36-cp36m-win32.whl", hash = "sha256:fca0e3a251908a499833aa292323f32437106001d436eca0e6e7833256674585"},
+    {file = "PyYAML-6.0.1-cp36-cp36m-win_amd64.whl", hash = "sha256:f22ac1c3cac4dbc50079e965eba2c1058622631e526bd9afd45fedd49ba781fa"},
+    {file = "PyYAML-6.0.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:b1275ad35a5d18c62a7220633c913e1b42d44b46ee12554e5fd39c70a243d6a3"},
+    {file = "PyYAML-6.0.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:18aeb1bf9a78867dc38b259769503436b7c72f7a1f1f4c93ff9a17de54319b27"},
+    {file = "PyYAML-6.0.1-cp37-cp37m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:596106435fa6ad000c2991a98fa58eeb8656ef2325d7e158344fb33864ed87e3"},
+    {file = "PyYAML-6.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:baa90d3f661d43131ca170712d903e6295d1f7a0f595074f151c0aed377c9b9c"},
+    {file = "PyYAML-6.0.1-cp37-cp37m-win32.whl", hash = "sha256:9046c58c4395dff28dd494285c82ba00b546adfc7ef001486fbf0324bc174fba"},
+    {file = "PyYAML-6.0.1-cp37-cp37m-win_amd64.whl", hash = "sha256:4fb147e7a67ef577a588a0e2c17b6db51dda102c71de36f8549b6816a96e1867"},
+    {file = "PyYAML-6.0.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:1d4c7e777c441b20e32f52bd377e0c409713e8bb1386e1099c2415f26e479595"},
+    {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5"},
+    {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696"},
+    {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735"},
+    {file = "PyYAML-6.0.1-cp38-cp38-win32.whl", hash = "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206"},
+    {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
+    {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
+    {file = "PyYAML-6.0.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5773183b6446b2c99bb77e77595dd486303b4faab2b086e7b17bc6bef28865f6"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:b786eecbdf8499b9ca1d697215862083bd6d2a99965554781d0d8d1ad31e13a0"},
+    {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-win32.whl", hash = "sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-win_amd64.whl", hash = "sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486"},
+    {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
 [[package]]
 name = "redis"
 version = "4.6.0"
 description = "Python client for Redis database and key-value store"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1322,7 +1285,6 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)"
 name = "requests"
 version = "2.31.0"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1344,7 +1306,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "rfc3986"
 version = "1.5.0"
 description = "Validating URI References per RFC 3986"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1359,7 +1320,6 @@ idna2008 = ["idna"]
 name = "s3transfer"
 version = "0.6.1"
 description = "An Amazon S3 Transfer Manager"
-category = "main"
 optional = false
 python-versions = ">= 3.7"
 files = [
@@ -1377,7 +1337,6 @@ crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"]
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1389,7 +1348,6 @@ files = [
 name = "smmap"
 version = "5.0.0"
 description = "A pure Python implementation of a sliding window memory map manager"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1401,7 +1359,6 @@ files = [
 name = "soupsieve"
 version = "2.4.1"
 description = "A modern CSS selector implementation for Beautiful Soup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1413,7 +1370,6 @@ files = [
 name = "structlog"
 version = "19.2.0"
 description = "Structured Logging for Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1434,7 +1390,6 @@ tests = ["coverage", "freezegun (>=0.2.8)", "pretend", "pytest (>=3.3.0)", "pyth
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
-category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1446,7 +1401,6 @@ files = [
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1458,7 +1412,6 @@ files = [
 name = "tqdm"
 version = "4.65.0"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1479,7 +1432,6 @@ telegram = ["requests"]
 name = "typing-extensions"
 version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1491,7 +1443,6 @@ files = [
 name = "urllib3"
 version = "1.26.16"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -1508,7 +1459,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 name = "waitress"
 version = "2.1.2"
 description = "Waitress WSGI server"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -1524,7 +1474,6 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"]
 name = "webob"
 version = "1.8.7"
 description = "WSGI request and response object"
-category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*"
 files = [
@@ -1540,7 +1489,6 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"]
 name = "websocket-client"
 version = "1.6.1"
 description = "WebSocket client for Python with low level API options"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1557,7 +1505,6 @@ test = ["websockets"]
 name = "webtest"
 version = "2.0.35"
 description = "Helper to test WSGI applications"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1579,7 +1526,6 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 name = "zipp"
 version = "3.15.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1594,4 +1540,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.7,<3.10"
-content-hash = "b8d6612bb28cfb9da79306a82b2ac35a20678e1f62ef86c93b8af3c3d1ed798e"
+content-hash = "71787cfc2bcda8e08be58628428cdeff84f8a05c50d70dd88d090b5d8ea41354"
diff --git a/pyproject.toml b/pyproject.toml
index f31d26f91..deb40e15a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,7 +46,7 @@ aws-requests-auth = ">=0.4.2,<1"
 docker = "^4.4.4"
 gitpython = "^3.1.2"
 pytz = ">=2020.4"
-PyYAML = ">=5.1,<5.5"
+PyYAML = "^6.0.1"
 requests = "^2.21.0"
 rfc3986 = "^1.4.0"
 structlog = "^19.2.0"

From ece924a468b4892187ba6d808155eae02b76914e Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 22 Aug 2023 15:41:12 -0400
Subject: [PATCH 02/35] Up pyyaml version to ^6.0.1 for Mac M1 issue with
 build.

---
 CHANGELOG.rst  | 6 ++++++
 pyproject.toml | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 8cae87006..e510e201e 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,6 +7,12 @@ Change Log
 ----------
 
 
+7.9.0
+=====
+
+* Changed ``PyYAML`` version to ^6.0.1; the Mac M1 has issues building 5.4.1 (though 5.3.1 works).
+
+
 7.8.0
 =====
 
diff --git a/pyproject.toml b/pyproject.toml
index deb40e15a..81dde5a1b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.8.0"
+version = "7.9.0"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From 4a8f0519ad4466343a31864dcd688189fb551a2d Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 24 Aug 2023 09:41:59 -0400
Subject: [PATCH 03/35] CHANGELOG changes.

---
 CHANGELOG.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e510e201e..55cf86a42 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -10,7 +10,11 @@ Change Log
 7.9.0
 =====
 
-* Changed ``PyYAML`` version to ^6.0.1; the Mac M1 has issues building 5.4.1 (though 5.3.1 works).
+* Changed PyYAML version to ^6.0.1; Mac M1 has issues building 5.4.1 (though 5.3.1 works).
+  See PyYAML 6.0 change log here: https://github.com/yaml/pyyaml/blob/master/CHANGES
+  The only incompatible change seems to be that yaml.load now requires a Loader argument;
+  and searching our repos (4dn-dcic, dbmi-bgm, smaht-dac) the only ones which might be affected
+  are cwltools and parliament2, neither of which are dependent on dcicutils in any way.
 
 
 7.8.0

From 2f49bcb3c287cd9a8b7bd67c58b23773de71cd0a Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 25 Aug 2023 07:46:23 -0400
Subject: [PATCH 04/35] version update

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8afb4271b..9abefe042 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.9.0.1b1"  # TODO: To become 7.10.0
+version = "7.9.0.2b1"  # TODO: To become 7.10.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From 829e5b015873d804df0f3dff5fbecced34b86a7b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 25 Aug 2023 13:27:02 -0400
Subject: [PATCH 05/35] Fix to test_s3_utils from
 kmp_sheet_utils_schema_hinting branch.

---
 pyproject.toml        | 2 +-
 test/test_s3_utils.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9abefe042..0836a8cee 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.9.0.2b1"  # TODO: To become 7.10.0
+version = "7.9.0.2b2"  # TODO: To become 7.10.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
diff --git a/test/test_s3_utils.py b/test/test_s3_utils.py
index 3cfd05c7e..30fa207c3 100644
--- a/test/test_s3_utils.py
+++ b/test/test_s3_utils.py
@@ -409,7 +409,7 @@ def test_s3utils_get_google_key():
     keys = s3u.get_google_key()
     assert isinstance(keys, dict)
     assert keys['type'] == 'service_account'
-    assert keys["project_id"] == "fourdn-fourfront"
+    assert keys["project_id"] == "fourfront-396315" # yes, this is a magic constant
     for dict_key in ['private_key_id', 'private_key', 'client_email', 'client_id', 'auth_uri', 'client_x509_cert_url']:
         assert keys[dict_key]
 

From 53c8e6d2d6761600d00becab56153177476d5582 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 25 Aug 2023 13:32:20 -0400
Subject: [PATCH 06/35] flake8 update

---
 test/test_s3_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/test_s3_utils.py b/test/test_s3_utils.py
index 30fa207c3..0e98959cd 100644
--- a/test/test_s3_utils.py
+++ b/test/test_s3_utils.py
@@ -409,7 +409,7 @@ def test_s3utils_get_google_key():
     keys = s3u.get_google_key()
     assert isinstance(keys, dict)
     assert keys['type'] == 'service_account'
-    assert keys["project_id"] == "fourfront-396315" # yes, this is a magic constant
+    assert keys["project_id"] == "fourfront-396315"  # yes, this is a magic constant
     for dict_key in ['private_key_id', 'private_key', 'client_email', 'client_id', 'auth_uri', 'client_x509_cert_url']:
         assert keys[dict_key]
 

From 6cc26bc4b02f5df5eb3a0a21b60c7fe6bffcc5f1 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 10:03:00 -0400
Subject: [PATCH 07/35] Update to Python 3.11!

---
 CHANGELOG.rst  |   5 +-
 poetry.lock    | 129 +++++++++++++++++++++++++------------------------
 pyproject.toml |   4 +-
 3 files changed, 71 insertions(+), 67 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 584f52ddd..e8571ab3f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -6,9 +6,10 @@ dcicutils
 Change Log
 ----------
 
-7.13.0
-======
+8.0.0
+=====
 
+* Update Python to 3.11.
 * Changed PyYAML version to ^6.0.1; Mac M1 has issues building 5.4.1 (though 5.3.1 works).
   See PyYAML 6.0 change log here: https://github.com/yaml/pyyaml/blob/master/CHANGES
   The only incompatible change seems to be that yaml.load now requires a Loader argument;
diff --git a/poetry.lock b/poetry.lock
index 1a4b10c74..50d2b0955 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,13 +2,13 @@
 
 [[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.dependencies]
@@ -48,17 +48,17 @@ lxml = ["lxml"]
 
 [[package]]
 name = "boto3"
-version = "1.28.20"
+version = "1.28.51"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.20-py3-none-any.whl", hash = "sha256:a654d57e3882e7fd2c1260d604a44364a2fed00da4f52faf37e5901e71145df1"},
-    {file = "boto3-1.28.20.tar.gz", hash = "sha256:e3c2e8e55c17af6671a5332d6ab4635ad9793c80d0ac6d78af7b30a994d0681b"},
+    {file = "boto3-1.28.51-py3-none-any.whl", hash = "sha256:8149f17587c68e556743018f213f00ece81a0f021adb9b9b697a2ee8802583d7"},
+    {file = "boto3-1.28.51.tar.gz", hash = "sha256:8860ab54a26d1d596d64fc9de7e40c4d7c53c100311208cbd90d9272c3385513"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.20,<1.32.0"
+botocore = ">=1.31.51,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.6.0,<0.7.0"
 
@@ -362,13 +362,13 @@ xray = ["mypy-boto3-xray (>=1.18.18)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.20"
+version = "1.31.51"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.20-py3-none-any.whl", hash = "sha256:be51c5352162700e7beb0aa27af394adbbf86f8e7a2ca0c437d448d0a7b2bdfb"},
-    {file = "botocore-1.31.20.tar.gz", hash = "sha256:485ef175cd011ebc965f4577d8cc02a226c46bd608dd2bb75ce6938328cff0fd"},
+    {file = "botocore-1.31.51-py3-none-any.whl", hash = "sha256:91dfb38801d45214875a892bd1e908fc7a894c2ed170bacd67e6929af72f2bd2"},
+    {file = "botocore-1.31.51.tar.gz", hash = "sha256:8e133add22f07b55d21e14176b97b82e993d5f9aca70f5b0cd0908cb105ba53a"},
 ]
 
 [package.dependencies]
@@ -652,34 +652,34 @@ toml = ["tomli"]
 
 [[package]]
 name = "cryptography"
-version = "41.0.3"
+version = "41.0.4"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "cryptography-41.0.4-pp39-pypy39_pp73-macosx_10_12_x86_64.whl", hash = "sha256:c3391bd8e6de35f6f1140e50aaeb3e2b3d6a9012536ca23ab0d9c35ec18c8a91"},
+    {file = "cryptography-41.0.4-pp39-pypy39_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:0d9409894f495d465fe6fda92cb70e8323e9648af912d5b9141d616df40a87b8"},
+    {file = "cryptography-41.0.4-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:8ac4f9ead4bbd0bc8ab2d318f97d85147167a488be0e08814a37eb2f439d5cf6"},
+    {file = "cryptography-41.0.4-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:047c4603aeb4bbd8db2756e38f5b8bd7e94318c047cfe4efeb5d715e08b49311"},
+    {file = "cryptography-41.0.4.tar.gz", hash = "sha256:7febc3094125fc126a7f6fb1f420d0da639f3f32cb15c8ff0dc3997c4549f51a"},
 ]
 
 [package.dependencies]
@@ -739,13 +739,13 @@ requests = ["requests (>=2.4.0,<3.0.0)"]
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.2"
+version = "1.1.3"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.2-py3-none-any.whl", hash = "sha256:e346e69d186172ca7cf029c8c1d16235aa0e04035e5750b4b95039e65204328f"},
-    {file = "exceptiongroup-1.1.2.tar.gz", hash = "sha256:12c3e887d6485d16943a309616de20ae5582633e0a2eda17f4e10fd61c1e8af5"},
+    {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"},
+    {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"},
 ]
 
 [package.extras]
@@ -795,19 +795,22 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.32"
+version = "3.1.36"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "GitPython-3.1.32-py3-none-any.whl", hash = "sha256:e3d59b1c2c6ebb9dfa7a184daf3b6dd4914237e7488a1730a6d8f6f5d0b4187f"},
-    {file = "GitPython-3.1.32.tar.gz", hash = "sha256:8d9b8cb1e80b9735e8717c9362079d3ce4c6e5ddeebedd0361b228c3a67a62f6"},
+    {file = "GitPython-3.1.36-py3-none-any.whl", hash = "sha256:8d22b5cfefd17c79914226982bb7851d6ade47545b1735a9d010a2a4c26d8388"},
+    {file = "GitPython-3.1.36.tar.gz", hash = "sha256:4bb0c2a6995e85064140d31a33289aa5dce80133a23d36fcd372d716c54d3ebf"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 typing-extensions = {version = ">=3.7.4.3", markers = "python_version < \"3.8\""}
 
+[package.extras]
+test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar", "virtualenv"]
+
 [[package]]
 name = "idna"
 version = "3.4"
@@ -887,13 +890,13 @@ psutil = {version = ">=4.0.0", markers = "sys_platform != \"cygwin\""}
 
 [[package]]
 name = "opensearch-py"
-version = "2.3.0"
+version = "2.3.1"
 description = "Python client for OpenSearch"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4"
 files = [
-    {file = "opensearch-py-2.3.0.tar.gz", hash = "sha256:493b224d0f865f62663f689c3a7662b1edccf9ee6c7643f2561cafda04e3a66a"},
-    {file = "opensearch_py-2.3.0-py2.py3-none-any.whl", hash = "sha256:4093d0bbe575979d67cfd74a153eb91d82e354e232d76c6980876321c73056c1"},
+    {file = "opensearch-py-2.3.1.tar.gz", hash = "sha256:f82a2e914835f7d645a632777de9a62d0c0de60ffd2f8cdae2ccfa4cfc40a185"},
+    {file = "opensearch_py-2.3.1-py2.py3-none-any.whl", hash = "sha256:eafbc5d56a7ca696afba7d77bcda1bbb849050cbf9265d57d8476576cb576395"},
 ]
 
 [package.dependencies]
@@ -1075,13 +1078,13 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"]
 
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "7.4.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"},
-    {file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"},
+    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
+    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
 ]
 
 [package.dependencies]
@@ -1182,13 +1185,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2023.3-py2.py3-none-any.whl", hash = "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb"},
-    {file = "pytz-2023.3.tar.gz", hash = "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588"},
+    {file = "pytz-2023.3.post1-py2.py3-none-any.whl", hash = "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"},
+    {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"},
 ]
 
 [[package]]
@@ -1318,13 +1321,13 @@ idna2008 = ["idna"]
 
 [[package]]
 name = "s3transfer"
-version = "0.6.1"
+version = "0.6.2"
 description = "An Amazon S3 Transfer Manager"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "s3transfer-0.6.1-py3-none-any.whl", hash = "sha256:3c0da2d074bf35d6870ef157158641178a4204a6e689e82546083e31e0311346"},
-    {file = "s3transfer-0.6.1.tar.gz", hash = "sha256:640bb492711f4c0c0905e1f62b6aaeb771881935ad27884852411f8e9cacbca9"},
+    {file = "s3transfer-0.6.2-py3-none-any.whl", hash = "sha256:b014be3a8a2aab98cfe1abc7229cc5a9a0cf05eb9c1f2b86b230fd8df3f78084"},
+    {file = "s3transfer-0.6.2.tar.gz", hash = "sha256:cab66d3380cca3e70939ef2255d01cd8aece6a4907a9528740f668c4b0611861"},
 ]
 
 [package.dependencies]
@@ -1346,13 +1349,13 @@ files = [
 
 [[package]]
 name = "smmap"
-version = "5.0.0"
+version = "5.0.1"
 description = "A pure Python implementation of a sliding window memory map manager"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "smmap-5.0.0-py3-none-any.whl", hash = "sha256:2aba19d6a040e78d8b09de5c57e96207b09ed71d8e55ce0959eeee6c8e190d94"},
-    {file = "smmap-5.0.0.tar.gz", hash = "sha256:c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936"},
+    {file = "smmap-5.0.1-py3-none-any.whl", hash = "sha256:e6d8668fa5f93e706934a62d7b4db19c8d9eb8cf2adbb75ef1b675aa332b69da"},
+    {file = "smmap-5.0.1.tar.gz", hash = "sha256:dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62"},
 ]
 
 [[package]]
@@ -1410,20 +1413,20 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.65.0"
+version = "4.66.1"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.65.0-py3-none-any.whl", hash = "sha256:c4f53a17fe37e132815abceec022631be8ffe1b9381c2e6e30aa70edc99e9671"},
-    {file = "tqdm-4.65.0.tar.gz", hash = "sha256:1871fb68a86b8fb3b59ca4cdd3dcccbc7e6d613eeed31f4c332531977b89beb5"},
+    {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"},
+    {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"},
 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["py-make (>=0.1.0)", "twine", "wheel"]
+dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
@@ -1539,5 +1542,5 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.7,<3.10"
-content-hash = "71787cfc2bcda8e08be58628428cdeff84f8a05c50d70dd88d090b5d8ea41354"
+python-versions = ">=3.7,<3.12"
+content-hash = "a5f5751f79e922ffa089a460c9f287ed66b152e74862f329f1fc9346fb411754"
diff --git a/pyproject.toml b/pyproject.toml
index 6e1cc45de..002dcb396 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b1"  # TODO: To become 7.13.0
+version = "7.12.0.1b3"  # TODO: To become 8.0.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -36,7 +36,7 @@ classifiers = [
 
 
 [tool.poetry.dependencies]
-python = ">=3.7,<3.10"
+python = ">=3.7,<3.12"
 boto3 = "^1.17.39"
 botocore = "^1.20.39"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.

From abe214017fe9231ecb772ec901cf5953a1b0619b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 10:32:11 -0400
Subject: [PATCH 08/35] Update to Python 3.11!

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 002dcb396..9bc2fcbf9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b3"  # TODO: To become 8.0.0
+version = "8.0.0"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From a7fa068c2f16b8fe0800c2bf72dda8a055da6835 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 13:08:26 -0400
Subject: [PATCH 09/35] Update boto3/botocore versions.

---
 CHANGELOG.rst  |   3 +-
 poetry.lock    | 686 ++++++++++++++++++++++++++++---------------------
 pyproject.toml |   8 +-
 3 files changed, 401 insertions(+), 296 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e8571ab3f..052595d9f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -10,7 +10,8 @@ Change Log
 =====
 
 * Update Python to 3.11.
-* Changed PyYAML version to ^6.0.1; Mac M1 has issues building 5.4.1 (though 5.3.1 works).
+* Updated boto3/botocore versions.
+* Updatad pyyaml version to ^6.0.1; Mac M1 has issues building 5.4.1 (though 5.3.1 works).
   See PyYAML 6.0 change log here: https://github.com/yaml/pyyaml/blob/master/CHANGES
   The only incompatible change seems to be that yaml.load now requires a Loader argument;
   and searching our repos (4dn-dcic, dbmi-bgm, smaht-dac) the only ones which might be affected
diff --git a/poetry.lock b/poetry.lock
index 50d2b0955..ca3b2cf34 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -67,298 +67,379 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "boto3-stubs"
-version = "1.18.23"
-description = "Type annotations for boto3 1.18.23, generated by mypy-boto3-builder 5.1.0"
+version = "1.28.51"
+description = "Type annotations for boto3 1.28.51 generated with mypy-boto3-builder 7.19.0"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "boto3-stubs-1.18.23.tar.gz", hash = "sha256:38915f107b36160ff2ba749fdb0de49d6dca4214fb16564d4f31f22f4f25099c"},
-    {file = "boto3_stubs-1.18.23-py3-none-any.whl", hash = "sha256:4bed5a3aa0a3c9516791b22e9cd0aba7b93dd4d30669fc032118568bcf678a36"},
+    {file = "boto3-stubs-1.28.51.tar.gz", hash = "sha256:6ebd53a356faaf576b3dd77c0923ab725b51da46d85adf6e2a89569b360490c0"},
+    {file = "boto3_stubs-1.28.51-py3-none-any.whl", hash = "sha256:67608ad5ccd862494dc4aac8dc7596393f3d9cd2123a78bcd1f3ac46f3799cb3"},
 ]
 
 [package.dependencies]
 botocore-stubs = "*"
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+types-s3transfer = "*"
+typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.12\""}
 
 [package.extras]
-accessanalyzer = ["mypy-boto3-accessanalyzer (>=1.18.18)"]
-acm = ["mypy-boto3-acm (>=1.18.18)"]
-acm-pca = ["mypy-boto3-acm-pca (>=1.18.18)"]
-alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.18.18)"]
-all = ["mypy-boto3-accessanalyzer (>=1.18.18)", "mypy-boto3-acm (>=1.18.18)", "mypy-boto3-acm-pca (>=1.18.18)", "mypy-boto3-alexaforbusiness (>=1.18.18)", "mypy-boto3-amp (>=1.18.18)", "mypy-boto3-amplify (>=1.18.18)", "mypy-boto3-amplifybackend (>=1.18.18)", "mypy-boto3-apigateway (>=1.18.18)", "mypy-boto3-apigatewaymanagementapi (>=1.18.18)", "mypy-boto3-apigatewayv2 (>=1.18.18)", "mypy-boto3-appconfig (>=1.18.18)", "mypy-boto3-appflow (>=1.18.18)", "mypy-boto3-appintegrations (>=1.18.18)", "mypy-boto3-application-autoscaling (>=1.18.18)", "mypy-boto3-application-insights (>=1.18.18)", "mypy-boto3-applicationcostprofiler (>=1.18.18)", "mypy-boto3-appmesh (>=1.18.18)", "mypy-boto3-apprunner (>=1.18.18)", "mypy-boto3-appstream (>=1.18.18)", "mypy-boto3-appsync (>=1.18.18)", "mypy-boto3-athena (>=1.18.18)", "mypy-boto3-auditmanager (>=1.18.18)", "mypy-boto3-autoscaling (>=1.18.18)", "mypy-boto3-autoscaling-plans (>=1.18.18)", "mypy-boto3-backup (>=1.18.18)", "mypy-boto3-batch (>=1.18.18)", "mypy-boto3-braket (>=1.18.18)", "mypy-boto3-budgets (>=1.18.18)", "mypy-boto3-ce (>=1.18.18)", "mypy-boto3-chime (>=1.18.18)", "mypy-boto3-chime-sdk-identity (>=1.18.18)", "mypy-boto3-chime-sdk-messaging (>=1.18.18)", "mypy-boto3-cloud9 (>=1.18.18)", "mypy-boto3-clouddirectory (>=1.18.18)", "mypy-boto3-cloudformation (>=1.18.18)", "mypy-boto3-cloudfront (>=1.18.18)", "mypy-boto3-cloudhsm (>=1.18.18)", "mypy-boto3-cloudhsmv2 (>=1.18.18)", "mypy-boto3-cloudsearch (>=1.18.18)", "mypy-boto3-cloudsearchdomain (>=1.18.18)", "mypy-boto3-cloudtrail (>=1.18.18)", "mypy-boto3-cloudwatch (>=1.18.18)", "mypy-boto3-codeartifact (>=1.18.18)", "mypy-boto3-codebuild (>=1.18.18)", "mypy-boto3-codecommit (>=1.18.18)", "mypy-boto3-codedeploy (>=1.18.18)", "mypy-boto3-codeguru-reviewer (>=1.18.18)", "mypy-boto3-codeguruprofiler (>=1.18.18)", "mypy-boto3-codepipeline (>=1.18.18)", "mypy-boto3-codestar (>=1.18.18)", "mypy-boto3-codestar-connections (>=1.18.18)", "mypy-boto3-codestar-notifications (>=1.18.18)", "mypy-boto3-cognito-identity (>=1.18.18)", "mypy-boto3-cognito-idp (>=1.18.18)", "mypy-boto3-cognito-sync (>=1.18.18)", "mypy-boto3-comprehend (>=1.18.18)", "mypy-boto3-comprehendmedical (>=1.18.18)", "mypy-boto3-compute-optimizer (>=1.18.18)", "mypy-boto3-config (>=1.18.18)", "mypy-boto3-connect (>=1.18.18)", "mypy-boto3-connect-contact-lens (>=1.18.18)", "mypy-boto3-connectparticipant (>=1.18.18)", "mypy-boto3-cur (>=1.18.18)", "mypy-boto3-customer-profiles (>=1.18.18)", "mypy-boto3-databrew (>=1.18.18)", "mypy-boto3-dataexchange (>=1.18.18)", "mypy-boto3-datapipeline (>=1.18.18)", "mypy-boto3-datasync (>=1.18.18)", "mypy-boto3-dax (>=1.18.18)", "mypy-boto3-detective (>=1.18.18)", "mypy-boto3-devicefarm (>=1.18.18)", "mypy-boto3-devops-guru (>=1.18.18)", "mypy-boto3-directconnect (>=1.18.18)", "mypy-boto3-discovery (>=1.18.18)", "mypy-boto3-dlm (>=1.18.18)", "mypy-boto3-dms (>=1.18.18)", "mypy-boto3-docdb (>=1.18.18)", "mypy-boto3-ds (>=1.18.18)", "mypy-boto3-dynamodb (>=1.18.18)", "mypy-boto3-dynamodbstreams (>=1.18.18)", "mypy-boto3-ebs (>=1.18.18)", "mypy-boto3-ec2 (>=1.18.18)", "mypy-boto3-ec2-instance-connect (>=1.18.18)", "mypy-boto3-ecr (>=1.18.18)", "mypy-boto3-ecr-public (>=1.18.18)", "mypy-boto3-ecs (>=1.18.18)", "mypy-boto3-efs (>=1.18.18)", "mypy-boto3-eks (>=1.18.18)", "mypy-boto3-elastic-inference (>=1.18.18)", "mypy-boto3-elasticache (>=1.18.18)", "mypy-boto3-elasticbeanstalk (>=1.18.18)", "mypy-boto3-elastictranscoder (>=1.18.18)", "mypy-boto3-elb (>=1.18.18)", "mypy-boto3-elbv2 (>=1.18.18)", "mypy-boto3-emr (>=1.18.18)", "mypy-boto3-emr-containers (>=1.18.18)", "mypy-boto3-es (>=1.18.18)", "mypy-boto3-events (>=1.18.18)", "mypy-boto3-finspace (>=1.18.18)", "mypy-boto3-finspace-data (>=1.18.18)", "mypy-boto3-firehose (>=1.18.18)", "mypy-boto3-fis (>=1.18.18)", "mypy-boto3-fms (>=1.18.18)", "mypy-boto3-forecast (>=1.18.18)", "mypy-boto3-forecastquery (>=1.18.18)", "mypy-boto3-frauddetector (>=1.18.18)", "mypy-boto3-fsx (>=1.18.18)", "mypy-boto3-gamelift (>=1.18.18)", "mypy-boto3-glacier (>=1.18.18)", "mypy-boto3-globalaccelerator (>=1.18.18)", "mypy-boto3-glue (>=1.18.18)", "mypy-boto3-greengrass (>=1.18.18)", "mypy-boto3-greengrassv2 (>=1.18.18)", "mypy-boto3-groundstation (>=1.18.18)", "mypy-boto3-guardduty (>=1.18.18)", "mypy-boto3-health (>=1.18.18)", "mypy-boto3-healthlake (>=1.18.18)", "mypy-boto3-honeycode (>=1.18.18)", "mypy-boto3-iam (>=1.18.18)", "mypy-boto3-identitystore (>=1.18.18)", "mypy-boto3-imagebuilder (>=1.18.18)", "mypy-boto3-importexport (>=1.18.18)", "mypy-boto3-inspector (>=1.18.18)", "mypy-boto3-iot (>=1.18.18)", "mypy-boto3-iot-data (>=1.18.18)", "mypy-boto3-iot-jobs-data (>=1.18.18)", "mypy-boto3-iot1click-devices (>=1.18.18)", "mypy-boto3-iot1click-projects (>=1.18.18)", "mypy-boto3-iotanalytics (>=1.18.18)", "mypy-boto3-iotdeviceadvisor (>=1.18.18)", "mypy-boto3-iotevents (>=1.18.18)", "mypy-boto3-iotevents-data (>=1.18.18)", "mypy-boto3-iotfleethub (>=1.18.18)", "mypy-boto3-iotsecuretunneling (>=1.18.18)", "mypy-boto3-iotsitewise (>=1.18.18)", "mypy-boto3-iotthingsgraph (>=1.18.18)", "mypy-boto3-iotwireless (>=1.18.18)", "mypy-boto3-ivs (>=1.18.18)", "mypy-boto3-kafka (>=1.18.18)", "mypy-boto3-kendra (>=1.18.18)", "mypy-boto3-kinesis (>=1.18.18)", "mypy-boto3-kinesis-video-archived-media (>=1.18.18)", "mypy-boto3-kinesis-video-media (>=1.18.18)", "mypy-boto3-kinesis-video-signaling (>=1.18.18)", "mypy-boto3-kinesisanalytics (>=1.18.18)", "mypy-boto3-kinesisanalyticsv2 (>=1.18.18)", "mypy-boto3-kinesisvideo (>=1.18.18)", "mypy-boto3-kms (>=1.18.18)", "mypy-boto3-lakeformation (>=1.18.18)", "mypy-boto3-lambda (>=1.18.18)", "mypy-boto3-lex-models (>=1.18.18)", "mypy-boto3-lex-runtime (>=1.18.18)", "mypy-boto3-lexv2-models (>=1.18.18)", "mypy-boto3-lexv2-runtime (>=1.18.18)", "mypy-boto3-license-manager (>=1.18.18)", "mypy-boto3-lightsail (>=1.18.18)", "mypy-boto3-location (>=1.18.18)", "mypy-boto3-logs (>=1.18.18)", "mypy-boto3-lookoutequipment (>=1.18.18)", "mypy-boto3-lookoutmetrics (>=1.18.18)", "mypy-boto3-lookoutvision (>=1.18.18)", "mypy-boto3-machinelearning (>=1.18.18)", "mypy-boto3-macie (>=1.18.18)", "mypy-boto3-macie2 (>=1.18.18)", "mypy-boto3-managedblockchain (>=1.18.18)", "mypy-boto3-marketplace-catalog (>=1.18.18)", "mypy-boto3-marketplace-entitlement (>=1.18.18)", "mypy-boto3-marketplacecommerceanalytics (>=1.18.18)", "mypy-boto3-mediaconnect (>=1.18.18)", "mypy-boto3-mediaconvert (>=1.18.18)", "mypy-boto3-medialive (>=1.18.18)", "mypy-boto3-mediapackage (>=1.18.18)", "mypy-boto3-mediapackage-vod (>=1.18.18)", "mypy-boto3-mediastore (>=1.18.18)", "mypy-boto3-mediastore-data (>=1.18.18)", "mypy-boto3-mediatailor (>=1.18.18)", "mypy-boto3-meteringmarketplace (>=1.18.18)", "mypy-boto3-mgh (>=1.18.18)", "mypy-boto3-mgn (>=1.18.18)", "mypy-boto3-migrationhub-config (>=1.18.18)", "mypy-boto3-mobile (>=1.18.18)", "mypy-boto3-mq (>=1.18.18)", "mypy-boto3-mturk (>=1.18.18)", "mypy-boto3-mwaa (>=1.18.18)", "mypy-boto3-neptune (>=1.18.18)", "mypy-boto3-network-firewall (>=1.18.18)", "mypy-boto3-networkmanager (>=1.18.18)", "mypy-boto3-nimble (>=1.18.18)", "mypy-boto3-opsworks (>=1.18.18)", "mypy-boto3-opsworkscm (>=1.18.18)", "mypy-boto3-organizations (>=1.18.18)", "mypy-boto3-outposts (>=1.18.18)", "mypy-boto3-personalize (>=1.18.18)", "mypy-boto3-personalize-events (>=1.18.18)", "mypy-boto3-personalize-runtime (>=1.18.18)", "mypy-boto3-pi (>=1.18.18)", "mypy-boto3-pinpoint (>=1.18.18)", "mypy-boto3-pinpoint-email (>=1.18.18)", "mypy-boto3-pinpoint-sms-voice (>=1.18.18)", "mypy-boto3-polly (>=1.18.18)", "mypy-boto3-pricing (>=1.18.18)", "mypy-boto3-proton (>=1.18.18)", "mypy-boto3-qldb (>=1.18.18)", "mypy-boto3-qldb-session (>=1.18.18)", "mypy-boto3-quicksight (>=1.18.18)", "mypy-boto3-ram (>=1.18.18)", "mypy-boto3-rds (>=1.18.18)", "mypy-boto3-rds-data (>=1.18.18)", "mypy-boto3-redshift (>=1.18.18)", "mypy-boto3-redshift-data (>=1.18.18)", "mypy-boto3-rekognition (>=1.18.18)", "mypy-boto3-resource-groups (>=1.18.18)", "mypy-boto3-resourcegroupstaggingapi (>=1.18.18)", "mypy-boto3-robomaker (>=1.18.18)", "mypy-boto3-route53 (>=1.18.18)", "mypy-boto3-route53-recovery-cluster (>=1.18.18)", "mypy-boto3-route53-recovery-control-config (>=1.18.18)", "mypy-boto3-route53-recovery-readiness (>=1.18.18)", "mypy-boto3-route53domains (>=1.18.18)", "mypy-boto3-route53resolver (>=1.18.18)", "mypy-boto3-s3 (>=1.18.18)", "mypy-boto3-s3control (>=1.18.18)", "mypy-boto3-s3outposts (>=1.18.18)", "mypy-boto3-sagemaker (>=1.18.18)", "mypy-boto3-sagemaker-a2i-runtime (>=1.18.18)", "mypy-boto3-sagemaker-edge (>=1.18.18)", "mypy-boto3-sagemaker-featurestore-runtime (>=1.18.18)", "mypy-boto3-sagemaker-runtime (>=1.18.18)", "mypy-boto3-savingsplans (>=1.18.18)", "mypy-boto3-schemas (>=1.18.18)", "mypy-boto3-sdb (>=1.18.18)", "mypy-boto3-secretsmanager (>=1.18.18)", "mypy-boto3-securityhub (>=1.18.18)", "mypy-boto3-serverlessrepo (>=1.18.18)", "mypy-boto3-service-quotas (>=1.18.18)", "mypy-boto3-servicecatalog (>=1.18.18)", "mypy-boto3-servicecatalog-appregistry (>=1.18.18)", "mypy-boto3-servicediscovery (>=1.18.18)", "mypy-boto3-ses (>=1.18.18)", "mypy-boto3-sesv2 (>=1.18.18)", "mypy-boto3-shield (>=1.18.18)", "mypy-boto3-signer (>=1.18.18)", "mypy-boto3-sms (>=1.18.18)", "mypy-boto3-sms-voice (>=1.18.18)", "mypy-boto3-snow-device-management (>=1.18.18)", "mypy-boto3-snowball (>=1.18.18)", "mypy-boto3-sns (>=1.18.18)", "mypy-boto3-sqs (>=1.18.18)", "mypy-boto3-ssm (>=1.18.18)", "mypy-boto3-ssm-contacts (>=1.18.18)", "mypy-boto3-ssm-incidents (>=1.18.18)", "mypy-boto3-sso (>=1.18.18)", "mypy-boto3-sso-admin (>=1.18.18)", "mypy-boto3-sso-oidc (>=1.18.18)", "mypy-boto3-stepfunctions (>=1.18.18)", "mypy-boto3-storagegateway (>=1.18.18)", "mypy-boto3-sts (>=1.18.18)", "mypy-boto3-support (>=1.18.18)", "mypy-boto3-swf (>=1.18.18)", "mypy-boto3-synthetics (>=1.18.18)", "mypy-boto3-textract (>=1.18.18)", "mypy-boto3-timestream-query (>=1.18.18)", "mypy-boto3-timestream-write (>=1.18.18)", "mypy-boto3-transcribe (>=1.18.18)", "mypy-boto3-transfer (>=1.18.18)", "mypy-boto3-translate (>=1.18.18)", "mypy-boto3-waf (>=1.18.18)", "mypy-boto3-waf-regional (>=1.18.18)", "mypy-boto3-wafv2 (>=1.18.18)", "mypy-boto3-wellarchitected (>=1.18.18)", "mypy-boto3-workdocs (>=1.18.18)", "mypy-boto3-worklink (>=1.18.18)", "mypy-boto3-workmail (>=1.18.18)", "mypy-boto3-workmailmessageflow (>=1.18.18)", "mypy-boto3-workspaces (>=1.18.18)", "mypy-boto3-xray (>=1.18.18)"]
-amp = ["mypy-boto3-amp (>=1.18.18)"]
-amplify = ["mypy-boto3-amplify (>=1.18.18)"]
-amplifybackend = ["mypy-boto3-amplifybackend (>=1.18.18)"]
-apigateway = ["mypy-boto3-apigateway (>=1.18.18)"]
-apigatewaymanagementapi = ["mypy-boto3-apigatewaymanagementapi (>=1.18.18)"]
-apigatewayv2 = ["mypy-boto3-apigatewayv2 (>=1.18.18)"]
-appconfig = ["mypy-boto3-appconfig (>=1.18.18)"]
-appflow = ["mypy-boto3-appflow (>=1.18.18)"]
-appintegrations = ["mypy-boto3-appintegrations (>=1.18.18)"]
-application-autoscaling = ["mypy-boto3-application-autoscaling (>=1.18.18)"]
-application-insights = ["mypy-boto3-application-insights (>=1.18.18)"]
-applicationcostprofiler = ["mypy-boto3-applicationcostprofiler (>=1.18.18)"]
-appmesh = ["mypy-boto3-appmesh (>=1.18.18)"]
-apprunner = ["mypy-boto3-apprunner (>=1.18.18)"]
-appstream = ["mypy-boto3-appstream (>=1.18.18)"]
-appsync = ["mypy-boto3-appsync (>=1.18.18)"]
-athena = ["mypy-boto3-athena (>=1.18.18)"]
-auditmanager = ["mypy-boto3-auditmanager (>=1.18.18)"]
-autoscaling = ["mypy-boto3-autoscaling (>=1.18.18)"]
-autoscaling-plans = ["mypy-boto3-autoscaling-plans (>=1.18.18)"]
-backup = ["mypy-boto3-backup (>=1.18.18)"]
-batch = ["mypy-boto3-batch (>=1.18.18)"]
-braket = ["mypy-boto3-braket (>=1.18.18)"]
-budgets = ["mypy-boto3-budgets (>=1.18.18)"]
-ce = ["mypy-boto3-ce (>=1.18.18)"]
-chime = ["mypy-boto3-chime (>=1.18.18)"]
-chime-sdk-identity = ["mypy-boto3-chime-sdk-identity (>=1.18.18)"]
-chime-sdk-messaging = ["mypy-boto3-chime-sdk-messaging (>=1.18.18)"]
-cloud9 = ["mypy-boto3-cloud9 (>=1.18.18)"]
-clouddirectory = ["mypy-boto3-clouddirectory (>=1.18.18)"]
-cloudformation = ["mypy-boto3-cloudformation (>=1.18.18)"]
-cloudfront = ["mypy-boto3-cloudfront (>=1.18.18)"]
-cloudhsm = ["mypy-boto3-cloudhsm (>=1.18.18)"]
-cloudhsmv2 = ["mypy-boto3-cloudhsmv2 (>=1.18.18)"]
-cloudsearch = ["mypy-boto3-cloudsearch (>=1.18.18)"]
-cloudsearchdomain = ["mypy-boto3-cloudsearchdomain (>=1.18.18)"]
-cloudtrail = ["mypy-boto3-cloudtrail (>=1.18.18)"]
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+waf = ["mypy-boto3-waf (>=1.28.0,<1.29.0)"]
+waf-regional = ["mypy-boto3-waf-regional (>=1.28.0,<1.29.0)"]
+wafv2 = ["mypy-boto3-wafv2 (>=1.28.0,<1.29.0)"]
+wellarchitected = ["mypy-boto3-wellarchitected (>=1.28.0,<1.29.0)"]
+wisdom = ["mypy-boto3-wisdom (>=1.28.0,<1.29.0)"]
+workdocs = ["mypy-boto3-workdocs (>=1.28.0,<1.29.0)"]
+worklink = ["mypy-boto3-worklink (>=1.28.0,<1.29.0)"]
+workmail = ["mypy-boto3-workmail (>=1.28.0,<1.29.0)"]
+workmailmessageflow = ["mypy-boto3-workmailmessageflow (>=1.28.0,<1.29.0)"]
+workspaces = ["mypy-boto3-workspaces (>=1.28.0,<1.29.0)"]
+workspaces-web = ["mypy-boto3-workspaces-web (>=1.28.0,<1.29.0)"]
+xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"]
 
 [[package]]
 name = "botocore"
@@ -381,17 +462,18 @@ crt = ["awscrt (==0.16.26)"]
 
 [[package]]
 name = "botocore-stubs"
-version = "1.21.22"
-description = "Type annotations for botocore 1.21.22, generated by mypy-boto3-builder 5.1.0"
+version = "1.31.51"
+description = "Type annotations and code completion for botocore"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7,<4.0"
 files = [
-    {file = "botocore-stubs-1.21.22.tar.gz", hash = "sha256:10d97e57cd79c66b6b78fe0fcac3ab22e421af222c03e93afe3d05bdb5dadc48"},
-    {file = "botocore_stubs-1.21.22-py3-none-any.whl", hash = "sha256:41ce3ad97ffe04c07a7939367d47aa6a049f4e939e184433f44f03e7149a2920"},
+    {file = "botocore_stubs-1.31.51-py3-none-any.whl", hash = "sha256:a31d93723fab3cd40cefb3c82ce7fe86bb901ee52cee20424e949118028afc26"},
+    {file = "botocore_stubs-1.31.51.tar.gz", hash = "sha256:159a57ff41ed16940da6c3e0ee2f4d9571bc6d345a1f41b36a85a093dd15aeff"},
 ]
 
 [package.dependencies]
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+types-awscrt = "*"
+typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.9\""}
 
 [[package]]
 name = "certifi"
@@ -1431,6 +1513,28 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
+[[package]]
+name = "types-awscrt"
+version = "0.19.1"
+description = "Type annotations and code completion for awscrt"
+optional = false
+python-versions = ">=3.7,<4.0"
+files = [
+    {file = "types_awscrt-0.19.1-py3-none-any.whl", hash = "sha256:68fffeb75396e9e7614cd930b2d52295f680230774750907bcafb56f11514043"},
+    {file = "types_awscrt-0.19.1.tar.gz", hash = "sha256:61833aa140e724a9098025610f4b8cde3dcf65b842631d7447378f9f5db4e1fd"},
+]
+
+[[package]]
+name = "types-s3transfer"
+version = "0.6.2"
+description = "Type annotations and code completion for s3transfer"
+optional = false
+python-versions = ">=3.7,<4.0"
+files = [
+    {file = "types_s3transfer-0.6.2-py3-none-any.whl", hash = "sha256:1068877b6e59be5226fa3006ae64371ac9d5bc590dfdbd9c66fd0a075d3254ac"},
+    {file = "types_s3transfer-0.6.2.tar.gz", hash = "sha256:4ba9b483796fdcd026aa162ee03bdcedd2bf7d08e9387c820dcdd158b0102057"},
+]
+
 [[package]]
 name = "typing-extensions"
 version = "4.7.1"
@@ -1543,4 +1647,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.7,<3.12"
-content-hash = "a5f5751f79e922ffa089a460c9f287ed66b152e74862f329f1fc9346fb411754"
+content-hash = "9d34985f33c818a00e6a4c6be2ab1e142fa1b7cc96b715fc7596a4b906b50b95"
diff --git a/pyproject.toml b/pyproject.toml
index 9bc2fcbf9..e9d4d308f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,8 +37,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.7,<3.12"
-boto3 = "^1.17.39"
-botocore = "^1.20.39"
+boto3 = "^1.28.51"
+botocore = "^1.31.51"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.
 # This value is intentionally pinned and must not be changed casually.
 elasticsearch = "7.13.4"
@@ -62,8 +62,8 @@ tqdm = "^4.65.0"
 
 
 [tool.poetry.dev-dependencies]
-botocore-stubs = "1.21.22"
-boto3-stubs = "1.18.23"
+botocore-stubs = "^1.31.51"
+boto3-stubs = "^1.28.51"
 coverage = ">=7.2.3"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023

From 669e51f2c7a69c20bd0e99246f14ea445e0e41a8 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 13:09:34 -0400
Subject: [PATCH 10/35] Update boto3/botocore versions.

---
 CHANGELOG.rst  |   2 +-
 poetry.lock    | 206 ++++++++++++++++++-------------------------------
 pyproject.toml |   2 +-
 3 files changed, 77 insertions(+), 133 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 052595d9f..6ee0d6bda 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -9,7 +9,7 @@ Change Log
 8.0.0
 =====
 
-* Update Python to 3.11.
+* Update Python to 3.11; and nixed Python 3.7.
 * Updated boto3/botocore versions.
 * Updatad pyyaml version to ^6.0.1; Mac M1 has issues building 5.4.1 (though 5.3.1 works).
   See PyYAML 6.0 change log here: https://github.com/yaml/pyyaml/blob/master/CHANGES
diff --git a/poetry.lock b/poetry.lock
index ca3b2cf34..979c332f4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -11,9 +11,6 @@ files = [
     {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"},
 ]
 
-[package.dependencies]
-typing-extensions = {version = ">=3.6.5", markers = "python_version < \"3.8\""}
-
 [[package]]
 name = "aws-requests-auth"
 version = "0.4.3"
@@ -659,71 +656,63 @@ files = [
 
 [[package]]
 name = "coverage"
-version = "7.2.7"
+version = "7.3.1"
 description = "Code coverage measurement for Python"
 optional = false
-python-versions = ">=3.7"
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+    {file = "coverage-7.3.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:636a8ac0b044cfeccae76a36f3b18264edcc810a76a49884b96dd744613ec0b7"},
+    {file = "coverage-7.3.1-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:5d991e13ad2ed3aced177f524e4d670f304c8233edad3210e02c465351f785a0"},
+    {file = "coverage-7.3.1-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:586649ada7cf139445da386ab6f8ef00e6172f11a939fc3b2b7e7c9082052fa0"},
+    {file = "coverage-7.3.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:4aba512a15a3e1e4fdbfed2f5392ec221434a614cc68100ca99dcad7af29f3f8"},
+    {file = "coverage-7.3.1-cp39-cp39-win32.whl", hash = "sha256:6bc6f3f4692d806831c136c5acad5ccedd0262aa44c087c46b7101c77e139140"},
+    {file = "coverage-7.3.1-cp39-cp39-win_amd64.whl", hash = "sha256:553d7094cb27db58ea91332e8b5681bac107e7242c23f7629ab1316ee73c4981"},
+    {file = "coverage-7.3.1-pp38.pp39.pp310-none-any.whl", hash = "sha256:220eb51f5fb38dfdb7e5d54284ca4d0cd70ddac047d750111a68ab1798945194"},
+    {file = "coverage-7.3.1.tar.gz", hash = "sha256:6cb7fe1581deb67b782c153136541e20901aa312ceedaf1467dcb35255787952"},
 ]
 
 [package.dependencies]
@@ -845,7 +834,6 @@ files = [
 ]
 
 [package.dependencies]
-importlib-metadata = {version = ">=1.1.0,<4.3", markers = "python_version < \"3.8\""}
 mccabe = ">=0.7.0,<0.8.0"
 pycodestyle = ">=2.9.0,<2.10.0"
 pyflakes = ">=2.5.0,<2.6.0"
@@ -888,7 +876,6 @@ files = [
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
-typing-extensions = {version = ">=3.7.4.3", markers = "python_version < \"3.8\""}
 
 [package.extras]
 test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar", "virtualenv"]
@@ -904,25 +891,6 @@ files = [
     {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
 ]
 
-[[package]]
-name = "importlib-metadata"
-version = "4.2.0"
-description = "Read metadata from Python packages"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "importlib_metadata-4.2.0-py3-none-any.whl", hash = "sha256:057e92c15bc8d9e8109738a48db0ccb31b4d9d5cfbee5a8670879a30be66304b"},
-    {file = "importlib_metadata-4.2.0.tar.gz", hash = "sha256:b7e52a1f8dec14a75ea73e0891f3060099ca1d8e6a462a4dff11c3e119ea1b31"},
-]
-
-[package.dependencies]
-typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
-zipp = ">=0.5"
-
-[package.extras]
-docs = ["jaraco.packaging (>=8.2)", "rst.linker (>=1.9)", "sphinx"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pep517", "pyfakefs", "pytest (>=4.6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy"]
-
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -1024,18 +992,15 @@ test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"]
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pluggy-1.2.0-py3-none-any.whl", hash = "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849"},
-    {file = "pluggy-1.2.0.tar.gz", hash = "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"},
+    {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"},
+    {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"},
 ]
 
-[package.dependencies]
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
-
 [package.extras]
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
@@ -1131,9 +1096,6 @@ files = [
     {file = "PyJWT-2.8.0.tar.gz", hash = "sha256:57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de"},
 ]
 
-[package.dependencies]
-typing-extensions = {version = "*", markers = "python_version <= \"3.7\""}
-
 [package.extras]
 crypto = ["cryptography (>=3.4.0)"]
 dev = ["coverage[toml] (==5.0.4)", "cryptography (>=3.4.0)", "pre-commit", "pytest (>=6.0.0,<7.0.0)", "sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"]
@@ -1172,7 +1134,6 @@ files = [
 [package.dependencies]
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
-importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 iniconfig = "*"
 packaging = "*"
 pluggy = ">=0.12,<2.0"
@@ -1359,8 +1320,6 @@ files = [
 
 [package.dependencies]
 async-timeout = {version = ">=4.0.2", markers = "python_full_version <= \"3.11.2\""}
-importlib-metadata = {version = ">=1.0", markers = "python_version < \"3.8\""}
-typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 hiredis = ["hiredis (>=1.0.0)"]
@@ -1442,13 +1401,13 @@ files = [
 
 [[package]]
 name = "soupsieve"
-version = "2.4.1"
+version = "2.5"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
-    {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
+    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
+    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
 ]
 
 [[package]]
@@ -1537,13 +1496,13 @@ files = [
 
 [[package]]
 name = "typing-extensions"
-version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.8.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
-    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
 ]
 
 [[package]]
@@ -1594,17 +1553,17 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "websocket-client"
-version = "1.6.1"
+version = "1.6.3"
 description = "WebSocket client for Python with low level API options"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"},
-    {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"},
+    {file = "websocket-client-1.6.3.tar.gz", hash = "sha256:3aad25d31284266bcfcfd1fd8a743f63282305a364b8d0948a43bd606acc652f"},
+    {file = "websocket_client-1.6.3-py3-none-any.whl", hash = "sha256:6cfc30d051ebabb73a5fa246efdcc14c8fbebbd0330f8984ac3bb6d9edd2ad03"},
 ]
 
 [package.extras]
-docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"]
+docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"]
 optional = ["python-socks", "wsaccel"]
 test = ["websockets"]
 
@@ -1629,22 +1588,7 @@ WebOb = ">=1.2"
 docs = ["Sphinx (>=1.8.1)", "docutils", "pylons-sphinx-themes (>=1.0.8)"]
 tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyquery"]
 
-[[package]]
-name = "zipp"
-version = "3.15.0"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
-]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
-
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.7,<3.12"
-content-hash = "9d34985f33c818a00e6a4c6be2ab1e142fa1b7cc96b715fc7596a4b906b50b95"
+python-versions = ">=3.8,<3.12"
+content-hash = "2a0905193dde26f0213176eb3e7e77a2356874226478fb30e96dbf70fe1e6288"
diff --git a/pyproject.toml b/pyproject.toml
index e9d4d308f..f226e41c9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,7 @@ classifiers = [
 
 
 [tool.poetry.dependencies]
-python = ">=3.7,<3.12"
+python = ">=3.8,<3.12"
 boto3 = "^1.28.51"
 botocore = "^1.31.51"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.

From 4b70bd205dd549b339b757799aba6e88bc69e1ea Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 13:11:21 -0400
Subject: [PATCH 11/35] CHANGELOG comments

---
 CHANGELOG.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 6ee0d6bda..f890fefb2 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -14,8 +14,8 @@ Change Log
 * Updatad pyyaml version to ^6.0.1; Mac M1 has issues building 5.4.1 (though 5.3.1 works).
   See PyYAML 6.0 change log here: https://github.com/yaml/pyyaml/blob/master/CHANGES
   The only incompatible change seems to be that yaml.load now requires a Loader argument;
-  and searching our repos (4dn-dcic, dbmi-bgm, smaht-dac) the only ones which might be affected
-  are cwltools and parliament2, neither of which are dependent on dcicutils in any way.
+  and searching our GitHub organizations (4dn-dcic, dbmi-bgm, smaht-dac) the only ones which might
+  be affected are cwltools and parliament2, neither of which are dependent on dcicutils in any way.
 
 7.12.0
 ======

From 927862e0203b2f28730597fa43ec3e606d2d0b31 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 13:58:47 -0400
Subject: [PATCH 12/35] Update to Python 3.11

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f226e41c9..d9857f805 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.0.0"
+version = "7.12.0.1b1"  # TODO: To become 8.0.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From 702aedbbb869c91e268f68ca2b5feae456e96ec7 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 15:23:44 -0400
Subject: [PATCH 13/35] Remove Python 3.7 from pyproject and GA

---
 .github/workflows/main.yml | 2 +-
 pyproject.toml             | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6e7b00e50..d9d6dd741 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python_version: [3.7, 3.8, 3.9]
+        python_version: [3.8, 3.9, 3.11]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
diff --git a/pyproject.toml b/pyproject.toml
index d9857f805..533c25f95 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -29,7 +29,6 @@ classifiers = [
 
     # Specify the Python versions you support here.
     'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.7',
     'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',
 ]

From 5b4c84b4a40d1a7d6fe523ae7d490f51dc916b3b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 16:04:22 -0400
Subject: [PATCH 14/35] Updated pip-licenses

---
 poetry.lock    | 63 ++++++++++++++++++++++++++++++++++++--------------
 pyproject.toml |  3 ++-
 2 files changed, 48 insertions(+), 18 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 979c332f4..a7c5cddbc 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -973,22 +973,33 @@ files = [
     {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
+[[package]]
+name = "pip"
+version = "23.2.1"
+description = "The PyPA recommended tool for installing Python packages."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pip-23.2.1-py3-none-any.whl", hash = "sha256:7ccf472345f20d35bdc9d1841ff5f313260c2c33fe417f48c30ac46cccabf5be"},
+    {file = "pip-23.2.1.tar.gz", hash = "sha256:fb0bd5435b3200c602b5bf61d2d43c2f13c02e29c1707567ae7fbc514eb9faf2"},
+]
+
 [[package]]
 name = "pip-licenses"
-version = "3.5.5"
+version = "4.3.3"
 description = "Dump the software license list of Python packages installed with pip."
 optional = false
-python-versions = "~=3.7"
+python-versions = "~=3.8"
 files = [
-    {file = "pip-licenses-3.5.5.tar.gz", hash = "sha256:748cfd7aca6e05032f9fa85691301295f4d943e87955be6914ca49abe3c075a4"},
-    {file = "pip_licenses-3.5.5-py3-none-any.whl", hash = "sha256:6129c116bab2b202d90d6e3a96092df4ad84c0c4d57bb70192fc03f8bf06d181"},
+    {file = "pip-licenses-4.3.3.tar.gz", hash = "sha256:d14447094135eb5e43e4d9e1e3bcdb17a05751a9199df2d07f043a542c241c7a"},
+    {file = "pip_licenses-4.3.3-py3-none-any.whl", hash = "sha256:1b697cace3149d7d380307bb1f1e0505f0db98f25fada64d32b7e6240f37f72c"},
 ]
 
 [package.dependencies]
-PTable = "*"
+prettytable = ">=2.3.0"
 
 [package.extras]
-test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"]
+test = ["docutils", "mypy", "pytest-cov", "pytest-pycodestyle", "pytest-runner"]
 
 [[package]]
 name = "pluggy"
@@ -1016,6 +1027,23 @@ files = [
     {file = "port_for-0.7.1-py3-none-any.whl", hash = "sha256:8abdaa1a7810281b0cecf718a6319da5f8538fdae3a5101d1e9afd54da0baf8c"},
 ]
 
+[[package]]
+name = "prettytable"
+version = "3.9.0"
+description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "prettytable-3.9.0-py3-none-any.whl", hash = "sha256:a71292ab7769a5de274b146b276ce938786f56c31cf7cea88b6f3775d82fe8c8"},
+    {file = "prettytable-3.9.0.tar.gz", hash = "sha256:f4ed94803c23073a90620b201965e5dc0bccf1760b7a7eaf3158cab8aaffdf34"},
+]
+
+[package.dependencies]
+wcwidth = "*"
+
+[package.extras]
+tests = ["pytest", "pytest-cov", "pytest-lazy-fixture"]
+
 [[package]]
 name = "psutil"
 version = "5.9.5"
@@ -1042,16 +1070,6 @@ files = [
 [package.extras]
 test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 
-[[package]]
-name = "ptable"
-version = "0.9.2"
-description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
-optional = false
-python-versions = "*"
-files = [
-    {file = "PTable-0.9.2.tar.gz", hash = "sha256:aa7fc151cb40f2dabcd2275ba6f7fd0ff8577a86be3365cd3fb297cbe09cc292"},
-]
-
 [[package]]
 name = "pycodestyle"
 version = "2.9.1"
@@ -1536,6 +1554,17 @@ files = [
 docs = ["Sphinx (>=1.8.1)", "docutils", "pylons-sphinx-themes (>=1.0.9)"]
 testing = ["coverage (>=5.0)", "pytest", "pytest-cover"]
 
+[[package]]
+name = "wcwidth"
+version = "0.2.6"
+description = "Measures the displayed width of unicode strings in a terminal"
+optional = false
+python-versions = "*"
+files = [
+    {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"},
+    {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"},
+]
+
 [[package]]
 name = "webob"
 version = "1.8.7"
@@ -1591,4 +1620,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "2a0905193dde26f0213176eb3e7e77a2356874226478fb30e96dbf70fe1e6288"
+content-hash = "2a1757e11fe4e2414012568c90ecb567a60661888c7abbb67ef789e95086c12b"
diff --git a/pyproject.toml b/pyproject.toml
index 533c25f95..9aea80ccb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -69,7 +69,8 @@ coverage = ">=7.2.3"
 # coveralls = ">=3.3.1"
 flake8 = ">=3.9.2"
 flaky = ">=3.7.0"
-pip-licenses = "^3.5.5"
+pip-licenses = "^4.3.3"
+pip = "23.2.1"
 pytest = ">=4.5.0"
 pytest-cov = ">=2.7.1"
 pytest-mock = ">=1.11.0"

From 4120faac4c0f67f2215d53786756738fc257d58f Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 16:05:39 -0400
Subject: [PATCH 15/35] Updated pip-licenses

---
 poetry.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index a7c5cddbc..4444c55a2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1620,4 +1620,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "2a1757e11fe4e2414012568c90ecb567a60661888c7abbb67ef789e95086c12b"
+content-hash = "f1609df6edccf15316820b739ba7c460d6e35cd18693026d321aa2b78aa54d23"

From a25959bad7fd15349399caa00af610b48c242855 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 16:07:55 -0400
Subject: [PATCH 16/35] update python to 3.9 in static-checks.yml

---
 .github/workflows/static-checks.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/static-checks.yml b/.github/workflows/static-checks.yml
index 577ea9835..0d914f264 100644
--- a/.github/workflows/static-checks.yml
+++ b/.github/workflows/static-checks.yml
@@ -27,7 +27,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: 3.9
       - name: Python Package Setup
         run: |
           make configure

From 07bbdd08ed37aa7b52af77e8c32e34d49ef8a8d3 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 20 Sep 2023 17:33:24 -0400
Subject: [PATCH 17/35] Removed pip from pyproject

---
 poetry.lock    | 43 ++++++++++++++++---------------------------
 pyproject.toml |  1 -
 2 files changed, 16 insertions(+), 28 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 4444c55a2..43d756a9f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -45,17 +45,17 @@ lxml = ["lxml"]
 
 [[package]]
 name = "boto3"
-version = "1.28.51"
+version = "1.28.52"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.51-py3-none-any.whl", hash = "sha256:8149f17587c68e556743018f213f00ece81a0f021adb9b9b697a2ee8802583d7"},
-    {file = "boto3-1.28.51.tar.gz", hash = "sha256:8860ab54a26d1d596d64fc9de7e40c4d7c53c100311208cbd90d9272c3385513"},
+    {file = "boto3-1.28.52-py3-none-any.whl", hash = "sha256:1d36db102517d62c6968b3b0636303241f56859d12dd071def4882fc6e030b20"},
+    {file = "boto3-1.28.52.tar.gz", hash = "sha256:a34fc153cb2f6fb2f79a764286c967392e8aae9412381d943bddc576c4f7631a"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.51,<1.32.0"
+botocore = ">=1.31.52,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.6.0,<0.7.0"
 
@@ -64,13 +64,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "boto3-stubs"
-version = "1.28.51"
-description = "Type annotations for boto3 1.28.51 generated with mypy-boto3-builder 7.19.0"
+version = "1.28.52"
+description = "Type annotations for boto3 1.28.52 generated with mypy-boto3-builder 7.19.0"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "boto3-stubs-1.28.51.tar.gz", hash = "sha256:6ebd53a356faaf576b3dd77c0923ab725b51da46d85adf6e2a89569b360490c0"},
-    {file = "boto3_stubs-1.28.51-py3-none-any.whl", hash = "sha256:67608ad5ccd862494dc4aac8dc7596393f3d9cd2123a78bcd1f3ac46f3799cb3"},
+    {file = "boto3-stubs-1.28.52.tar.gz", hash = "sha256:12d7e5865aeec52e1f73b935b1c6a42e61325538fc2cb83a87a83e41e9485241"},
+    {file = "boto3_stubs-1.28.52-py3-none-any.whl", hash = "sha256:3ea81a225e062f3bcb205467891086ea031519697ad54622e61251b52609b8d6"},
 ]
 
 [package.dependencies]
@@ -114,7 +114,7 @@ backup-gateway = ["mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)"]
 backupstorage = ["mypy-boto3-backupstorage (>=1.28.0,<1.29.0)"]
 batch = ["mypy-boto3-batch (>=1.28.0,<1.29.0)"]
 billingconductor = ["mypy-boto3-billingconductor (>=1.28.0,<1.29.0)"]
-boto3 = ["boto3 (==1.28.51)", "botocore (==1.31.51)"]
+boto3 = ["boto3 (==1.28.52)", "botocore (==1.31.52)"]
 braket = ["mypy-boto3-braket (>=1.28.0,<1.29.0)"]
 budgets = ["mypy-boto3-budgets (>=1.28.0,<1.29.0)"]
 ce = ["mypy-boto3-ce (>=1.28.0,<1.29.0)"]
@@ -440,13 +440,13 @@ xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.51"
+version = "1.31.52"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.51-py3-none-any.whl", hash = "sha256:91dfb38801d45214875a892bd1e908fc7a894c2ed170bacd67e6929af72f2bd2"},
-    {file = "botocore-1.31.51.tar.gz", hash = "sha256:8e133add22f07b55d21e14176b97b82e993d5f9aca70f5b0cd0908cb105ba53a"},
+    {file = "botocore-1.31.52-py3-none-any.whl", hash = "sha256:46b0a75a38521aa6a75fddccb1542e002930e609d4e13516f40fef170d32e515"},
+    {file = "botocore-1.31.52.tar.gz", hash = "sha256:6d09881c5a8be34b497872ca3936f8757d886a6f42f2a8703411928189cfedc0"},
 ]
 
 [package.dependencies]
@@ -459,13 +459,13 @@ crt = ["awscrt (==0.16.26)"]
 
 [[package]]
 name = "botocore-stubs"
-version = "1.31.51"
+version = "1.31.52"
 description = "Type annotations and code completion for botocore"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
-    {file = "botocore_stubs-1.31.51-py3-none-any.whl", hash = "sha256:a31d93723fab3cd40cefb3c82ce7fe86bb901ee52cee20424e949118028afc26"},
-    {file = "botocore_stubs-1.31.51.tar.gz", hash = "sha256:159a57ff41ed16940da6c3e0ee2f4d9571bc6d345a1f41b36a85a093dd15aeff"},
+    {file = "botocore_stubs-1.31.52-py3-none-any.whl", hash = "sha256:11431ac0faa35cad6deed6e87002f312f8ea6358d8106a241b60bcead2f84279"},
+    {file = "botocore_stubs-1.31.52.tar.gz", hash = "sha256:2fa9b78c7a335a94d918079773dc3198786de741586187d847a8710b9c337009"},
 ]
 
 [package.dependencies]
@@ -973,17 +973,6 @@ files = [
     {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
 ]
 
-[[package]]
-name = "pip"
-version = "23.2.1"
-description = "The PyPA recommended tool for installing Python packages."
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "pip-23.2.1-py3-none-any.whl", hash = "sha256:7ccf472345f20d35bdc9d1841ff5f313260c2c33fe417f48c30ac46cccabf5be"},
-    {file = "pip-23.2.1.tar.gz", hash = "sha256:fb0bd5435b3200c602b5bf61d2d43c2f13c02e29c1707567ae7fbc514eb9faf2"},
-]
-
 [[package]]
 name = "pip-licenses"
 version = "4.3.3"
@@ -1620,4 +1609,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "f1609df6edccf15316820b739ba7c460d6e35cd18693026d321aa2b78aa54d23"
+content-hash = "0aff1a06a42172e53af4af12de567f74bf87dec1cdd16b62b99271bbed5ac8a6"
diff --git a/pyproject.toml b/pyproject.toml
index 9aea80ccb..09abc41fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,7 +70,6 @@ coverage = ">=7.2.3"
 flake8 = ">=3.9.2"
 flaky = ">=3.7.0"
 pip-licenses = "^4.3.3"
-pip = "23.2.1"
 pytest = ">=4.5.0"
 pytest-cov = ">=2.7.1"
 pytest-mock = ">=1.11.0"

From ba13cbf0c2af8fd2cbb8501dc49b06000584fec1 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 21 Sep 2023 11:43:39 -0400
Subject: [PATCH 18/35] Put pytest to latest version and added pytest-redis to
 ^3.0.2.

---
 poetry.lock    | 17 +++++++----------
 pyproject.toml |  4 ++--
 2 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 43d756a9f..81cd1d452 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1186,23 +1186,20 @@ dev = ["pre-commit", "pytest-asyncio", "tox"]
 
 [[package]]
 name = "pytest-redis"
-version = "2.4.0"
+version = "3.0.2"
 description = "Redis fixtures and fixture factories for Pytest."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pytest-redis-2.4.0.tar.gz", hash = "sha256:8a07520abed3cd341e8da1793059aa5717b02e56c43e7c76435db682cede10aa"},
-    {file = "pytest_redis-2.4.0-py3-none-any.whl", hash = "sha256:3cf00ad3f7241e38ce6f1bcb66af11b91956a889f1e216cfc026e81aa638a4e7"},
+    {file = "pytest-redis-3.0.2.tar.gz", hash = "sha256:e54660e95fb1ec0feb7426523e37710ac7850380c60f9ee693c4045a6fc28ac5"},
+    {file = "pytest_redis-3.0.2-py3-none-any.whl", hash = "sha256:e2fd39658f396b6ae22976b80f94c61ebda5bc2bb8fe7eabcc7a7f994f7659f8"},
 ]
 
 [package.dependencies]
 mirakuru = "*"
 port-for = ">=0.6.0"
-pytest = ">=6.2.0"
-redis = "*"
-
-[package.extras]
-tests = ["mock", "pytest-cov", "pytest-xdist"]
+pytest = ">=6.2"
+redis = ">=3"
 
 [[package]]
 name = "pytest-runner"
@@ -1609,4 +1606,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "0aff1a06a42172e53af4af12de567f74bf87dec1cdd16b62b99271bbed5ac8a6"
+content-hash = "fb29c53ae0f29eab1185dee384d1cd3b7dd039ca2cef7a5a38915de0e939a6a1"
diff --git a/pyproject.toml b/pyproject.toml
index 09abc41fa..473ed7d44 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,10 +70,10 @@ coverage = ">=7.2.3"
 flake8 = ">=3.9.2"
 flaky = ">=3.7.0"
 pip-licenses = "^4.3.3"
-pytest = ">=4.5.0"
+pytest = "^7.4.2"
 pytest-cov = ">=2.7.1"
 pytest-mock = ">=1.11.0"
-pytest-redis = "^2.0.0"
+pytest-redis = "^3.0.2"
 pytest-runner = ">=5.1"
 
 

From 7ed1511d7542bbacd6a72e9f881f82a1a259d9e6 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 21 Sep 2023 12:17:53 -0400
Subject: [PATCH 19/35] Update version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 473ed7d44..ac8a71e1e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b1"  # TODO: To become 8.0.0
+version = "7.12.0.1b5"  # TODO: To become 8.0.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From 88f3b8951769c0e12fff8dfb5375b95a2fef5105 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 26 Sep 2023 08:22:09 -0400
Subject: [PATCH 20/35] Updated boto versions.

---
 poetry.lock    | 40 ++++++++++++++++++++--------------------
 pyproject.toml |  8 ++++----
 2 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 81cd1d452..d0564a273 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -45,17 +45,17 @@ lxml = ["lxml"]
 
 [[package]]
 name = "boto3"
-version = "1.28.52"
+version = "1.28.54"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.52-py3-none-any.whl", hash = "sha256:1d36db102517d62c6968b3b0636303241f56859d12dd071def4882fc6e030b20"},
-    {file = "boto3-1.28.52.tar.gz", hash = "sha256:a34fc153cb2f6fb2f79a764286c967392e8aae9412381d943bddc576c4f7631a"},
+    {file = "boto3-1.28.54-py3-none-any.whl", hash = "sha256:3cb2aee317a1b8686e3b23674e4099b8ff7451bd8acc61b9719acff86fa024d1"},
+    {file = "boto3-1.28.54.tar.gz", hash = "sha256:22e37d8c4f2d97b5e5c6ccc1d9edc7760717990b0ba8b8ea17a58cc87e57c5c9"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.52,<1.32.0"
+botocore = ">=1.31.54,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.6.0,<0.7.0"
 
@@ -64,13 +64,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "boto3-stubs"
-version = "1.28.52"
-description = "Type annotations for boto3 1.28.52 generated with mypy-boto3-builder 7.19.0"
+version = "1.28.54"
+description = "Type annotations for boto3 1.28.54 generated with mypy-boto3-builder 7.19.0"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "boto3-stubs-1.28.52.tar.gz", hash = "sha256:12d7e5865aeec52e1f73b935b1c6a42e61325538fc2cb83a87a83e41e9485241"},
-    {file = "boto3_stubs-1.28.52-py3-none-any.whl", hash = "sha256:3ea81a225e062f3bcb205467891086ea031519697ad54622e61251b52609b8d6"},
+    {file = "boto3-stubs-1.28.54.tar.gz", hash = "sha256:cb6f6a6cca4826c2b5d61b0a3fcf9cb84d7924c120b7e1c670f08e21cc010425"},
+    {file = "boto3_stubs-1.28.54-py3-none-any.whl", hash = "sha256:a58a6ebd0767d7aa1f4ab6f3eec93388b20afff5c5b25c8fe8f866d85eda6f67"},
 ]
 
 [package.dependencies]
@@ -114,7 +114,7 @@ backup-gateway = ["mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)"]
 backupstorage = ["mypy-boto3-backupstorage (>=1.28.0,<1.29.0)"]
 batch = ["mypy-boto3-batch (>=1.28.0,<1.29.0)"]
 billingconductor = ["mypy-boto3-billingconductor (>=1.28.0,<1.29.0)"]
-boto3 = ["boto3 (==1.28.52)", "botocore (==1.31.52)"]
+boto3 = ["boto3 (==1.28.54)", "botocore (==1.31.54)"]
 braket = ["mypy-boto3-braket (>=1.28.0,<1.29.0)"]
 budgets = ["mypy-boto3-budgets (>=1.28.0,<1.29.0)"]
 ce = ["mypy-boto3-ce (>=1.28.0,<1.29.0)"]
@@ -440,13 +440,13 @@ xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.52"
+version = "1.31.54"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.52-py3-none-any.whl", hash = "sha256:46b0a75a38521aa6a75fddccb1542e002930e609d4e13516f40fef170d32e515"},
-    {file = "botocore-1.31.52.tar.gz", hash = "sha256:6d09881c5a8be34b497872ca3936f8757d886a6f42f2a8703411928189cfedc0"},
+    {file = "botocore-1.31.54-py3-none-any.whl", hash = "sha256:71fdb337ddcdb6bf378e1211cba9ce754c35f12b1524c7d0c0c147b2310356c7"},
+    {file = "botocore-1.31.54.tar.gz", hash = "sha256:c98e78a9490c4166b205f87912b46770e156bfe7d53bae54ccbd49c68a336ec6"},
 ]
 
 [package.dependencies]
@@ -459,13 +459,13 @@ crt = ["awscrt (==0.16.26)"]
 
 [[package]]
 name = "botocore-stubs"
-version = "1.31.52"
+version = "1.31.54"
 description = "Type annotations and code completion for botocore"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
-    {file = "botocore_stubs-1.31.52-py3-none-any.whl", hash = "sha256:11431ac0faa35cad6deed6e87002f312f8ea6358d8106a241b60bcead2f84279"},
-    {file = "botocore_stubs-1.31.52.tar.gz", hash = "sha256:2fa9b78c7a335a94d918079773dc3198786de741586187d847a8710b9c337009"},
+    {file = "botocore_stubs-1.31.54-py3-none-any.whl", hash = "sha256:6e3e015ba4d2172c6a9bd5ff5131c39c995991559a567dce6c8534884f83ded1"},
+    {file = "botocore_stubs-1.31.54.tar.gz", hash = "sha256:96223fdf87a68037dd1ed366ffe28b5b744aca495a365f4535e2179c9a88455c"},
 ]
 
 [package.dependencies]
@@ -865,20 +865,20 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.36"
+version = "3.1.37"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "GitPython-3.1.36-py3-none-any.whl", hash = "sha256:8d22b5cfefd17c79914226982bb7851d6ade47545b1735a9d010a2a4c26d8388"},
-    {file = "GitPython-3.1.36.tar.gz", hash = "sha256:4bb0c2a6995e85064140d31a33289aa5dce80133a23d36fcd372d716c54d3ebf"},
+    {file = "GitPython-3.1.37-py3-none-any.whl", hash = "sha256:5f4c4187de49616d710a77e98ddf17b4782060a1788df441846bddefbb89ab33"},
+    {file = "GitPython-3.1.37.tar.gz", hash = "sha256:f9b9ddc0761c125d5780eab2d64be4873fc6817c2899cbcb34b02344bdc7bc54"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
 [package.extras]
-test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar", "virtualenv"]
+test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar"]
 
 [[package]]
 name = "idna"
@@ -1606,4 +1606,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "fb29c53ae0f29eab1185dee384d1cd3b7dd039ca2cef7a5a38915de0e939a6a1"
+content-hash = "6cdcf4e9fab04bbcaa83c3054b61356b4830b55c67e2a362dd1af635ae75a688"
diff --git a/pyproject.toml b/pyproject.toml
index ac8a71e1e..288228385 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,8 +36,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.12"
-boto3 = "^1.28.51"
-botocore = "^1.31.51"
+boto3 = "^1.28.54"
+botocore = "^1.31.54"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.
 # This value is intentionally pinned and must not be changed casually.
 elasticsearch = "7.13.4"
@@ -61,8 +61,8 @@ tqdm = "^4.65.0"
 
 
 [tool.poetry.dev-dependencies]
-botocore-stubs = "^1.31.51"
-boto3-stubs = "^1.28.51"
+boto3-stubs = "^1.28.54"
+botocore-stubs = "^1.31.54"
 coverage = ">=7.2.3"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023

From 3e5cf5f4be1f2a9d0af835e521690af93c345e2c Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 26 Sep 2023 08:22:22 -0400
Subject: [PATCH 21/35] Updated boto versions.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 288228385..ccc85023e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b5"  # TODO: To become 8.0.0
+version = "7.12.0.1b6"  # TODO: To become 8.0.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From e24b3e04fa36d695f84c76c431f4d89a27a5b93c Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 07:03:24 -0400
Subject: [PATCH 22/35] Added Python 3.10, 3.11 to pyproject Python list

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ccc85023e..6ea1bef40 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b6"  # TODO: To become 8.0.0
+version = "7.12.0.1b7"  # TODO: To become 8.0.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -31,6 +31,8 @@ classifiers = [
     'Programming Language :: Python :: 3',
     'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11'
 ]
 
 

From c760707150588d65eb8085fb39eb0bf957910404 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 10:14:58 -0400
Subject: [PATCH 23/35] Update Ubuntu to 22.04 for GA

---
 .github/workflows/main.yml |  2 +-
 pyproject.toml             | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d9d6dd741..5ec18cdda 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,7 +20,7 @@ jobs:
     name: Test dcicutils with Python ${{ matrix.python_version }}
 
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python_version: [3.8, 3.9, 3.11]
diff --git a/pyproject.toml b/pyproject.toml
index 6ea1bef40..4597cbdb7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b7"  # TODO: To become 8.0.0
+version = "7.12.0.1b8"  # TODO: To become 8.0.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -38,8 +38,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.12"
-boto3 = "^1.28.54"
-botocore = "^1.31.54"
+boto3 = "^1.28.56"
+botocore = "^1.31.56"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.
 # This value is intentionally pinned and must not be changed casually.
 elasticsearch = "7.13.4"
@@ -63,8 +63,8 @@ tqdm = "^4.65.0"
 
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.28.54"
-botocore-stubs = "^1.31.54"
+boto3-stubs = "^1.28.56"
+botocore-stubs = "^1.31.56"
 coverage = ">=7.2.3"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023

From 7b3daafb46785295258dbed1f40252b9b519db40 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 10:17:15 -0400
Subject: [PATCH 24/35] Update Ubuntu to 22.04 for GA and poetry update

---
 poetry.lock | 46 +++++++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d0564a273..d7a42df51 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -45,32 +45,32 @@ lxml = ["lxml"]
 
 [[package]]
 name = "boto3"
-version = "1.28.54"
+version = "1.28.56"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.54-py3-none-any.whl", hash = "sha256:3cb2aee317a1b8686e3b23674e4099b8ff7451bd8acc61b9719acff86fa024d1"},
-    {file = "boto3-1.28.54.tar.gz", hash = "sha256:22e37d8c4f2d97b5e5c6ccc1d9edc7760717990b0ba8b8ea17a58cc87e57c5c9"},
+    {file = "boto3-1.28.56-py3-none-any.whl", hash = "sha256:f5fcb27cdbd08ca38d699f2d2e32d96d1d9fab3368c15c6bc326256612d2cfd7"},
+    {file = "boto3-1.28.56.tar.gz", hash = "sha256:b927a7ed335d543c33c15fa63f1076f3fa8422959771c2187da74bc4395ab6e3"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.54,<1.32.0"
+botocore = ">=1.31.56,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
-s3transfer = ">=0.6.0,<0.7.0"
+s3transfer = ">=0.7.0,<0.8.0"
 
 [package.extras]
 crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "boto3-stubs"
-version = "1.28.54"
-description = "Type annotations for boto3 1.28.54 generated with mypy-boto3-builder 7.19.0"
+version = "1.28.56"
+description = "Type annotations for boto3 1.28.56 generated with mypy-boto3-builder 7.19.0"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "boto3-stubs-1.28.54.tar.gz", hash = "sha256:cb6f6a6cca4826c2b5d61b0a3fcf9cb84d7924c120b7e1c670f08e21cc010425"},
-    {file = "boto3_stubs-1.28.54-py3-none-any.whl", hash = "sha256:a58a6ebd0767d7aa1f4ab6f3eec93388b20afff5c5b25c8fe8f866d85eda6f67"},
+    {file = "boto3-stubs-1.28.56.tar.gz", hash = "sha256:2b77d4b9e944ffa4308822dc0327269f47cc4527a97903a3c5d14b9abed4eaad"},
+    {file = "boto3_stubs-1.28.56-py3-none-any.whl", hash = "sha256:e9c1f32463cf8e6ba56588f7c0f5cae52190b87eb19744ad1067a717be1c80b3"},
 ]
 
 [package.dependencies]
@@ -114,7 +114,7 @@ backup-gateway = ["mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)"]
 backupstorage = ["mypy-boto3-backupstorage (>=1.28.0,<1.29.0)"]
 batch = ["mypy-boto3-batch (>=1.28.0,<1.29.0)"]
 billingconductor = ["mypy-boto3-billingconductor (>=1.28.0,<1.29.0)"]
-boto3 = ["boto3 (==1.28.54)", "botocore (==1.31.54)"]
+boto3 = ["boto3 (==1.28.56)", "botocore (==1.31.56)"]
 braket = ["mypy-boto3-braket (>=1.28.0,<1.29.0)"]
 budgets = ["mypy-boto3-budgets (>=1.28.0,<1.29.0)"]
 ce = ["mypy-boto3-ce (>=1.28.0,<1.29.0)"]
@@ -440,13 +440,13 @@ xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.54"
+version = "1.31.56"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.54-py3-none-any.whl", hash = "sha256:71fdb337ddcdb6bf378e1211cba9ce754c35f12b1524c7d0c0c147b2310356c7"},
-    {file = "botocore-1.31.54.tar.gz", hash = "sha256:c98e78a9490c4166b205f87912b46770e156bfe7d53bae54ccbd49c68a336ec6"},
+    {file = "botocore-1.31.56-py3-none-any.whl", hash = "sha256:66c686e4eda7051ffcc9357d9075390c8ab2f95a2977669039618ee186fb533b"},
+    {file = "botocore-1.31.56.tar.gz", hash = "sha256:70252cd8abc2fe9b791328e187620f5a3911545e2520486b01ecfad31f41b9cb"},
 ]
 
 [package.dependencies]
@@ -459,13 +459,13 @@ crt = ["awscrt (==0.16.26)"]
 
 [[package]]
 name = "botocore-stubs"
-version = "1.31.54"
+version = "1.31.56"
 description = "Type annotations and code completion for botocore"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
-    {file = "botocore_stubs-1.31.54-py3-none-any.whl", hash = "sha256:6e3e015ba4d2172c6a9bd5ff5131c39c995991559a567dce6c8534884f83ded1"},
-    {file = "botocore_stubs-1.31.54.tar.gz", hash = "sha256:96223fdf87a68037dd1ed366ffe28b5b744aca495a365f4535e2179c9a88455c"},
+    {file = "botocore_stubs-1.31.56-py3-none-any.whl", hash = "sha256:e8f7273f57c09ef47f8bdc89765b151f43a46b3c29c52fb58e9982115ed14d84"},
+    {file = "botocore_stubs-1.31.56.tar.gz", hash = "sha256:e1510bd361acf755ecace42ee984281adfea6f96695ed22a08a4ceeabfe66f5f"},
 ]
 
 [package.dependencies]
@@ -1366,13 +1366,13 @@ idna2008 = ["idna"]
 
 [[package]]
 name = "s3transfer"
-version = "0.6.2"
+version = "0.7.0"
 description = "An Amazon S3 Transfer Manager"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "s3transfer-0.6.2-py3-none-any.whl", hash = "sha256:b014be3a8a2aab98cfe1abc7229cc5a9a0cf05eb9c1f2b86b230fd8df3f78084"},
-    {file = "s3transfer-0.6.2.tar.gz", hash = "sha256:cab66d3380cca3e70939ef2255d01cd8aece6a4907a9528740f668c4b0611861"},
+    {file = "s3transfer-0.7.0-py3-none-any.whl", hash = "sha256:10d6923c6359175f264811ef4bf6161a3156ce8e350e705396a7557d6293c33a"},
+    {file = "s3transfer-0.7.0.tar.gz", hash = "sha256:fd3889a66f5fe17299fe75b82eae6cf722554edca744ca5d5fe308b104883d2e"},
 ]
 
 [package.dependencies]
@@ -1489,13 +1489,13 @@ files = [
 
 [[package]]
 name = "types-s3transfer"
-version = "0.6.2"
+version = "0.7.0"
 description = "Type annotations and code completion for s3transfer"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
-    {file = "types_s3transfer-0.6.2-py3-none-any.whl", hash = "sha256:1068877b6e59be5226fa3006ae64371ac9d5bc590dfdbd9c66fd0a075d3254ac"},
-    {file = "types_s3transfer-0.6.2.tar.gz", hash = "sha256:4ba9b483796fdcd026aa162ee03bdcedd2bf7d08e9387c820dcdd158b0102057"},
+    {file = "types_s3transfer-0.7.0-py3-none-any.whl", hash = "sha256:ae9ed9273465d9f43da8b96307383da410c6b59c3b2464c88d20b578768e97c6"},
+    {file = "types_s3transfer-0.7.0.tar.gz", hash = "sha256:aca0f2486d0a3a5037cd5b8f3e20a4522a29579a8dd183281ff0aa1c4e2c8aa7"},
 ]
 
 [[package]]
@@ -1606,4 +1606,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "6cdcf4e9fab04bbcaa83c3054b61356b4830b55c67e2a362dd1af635ae75a688"
+content-hash = "cf533f908fb4f451ada1932dfa17d6c47beb8052126bf286ee82a4fa3eb1cc65"

From 099a32e7869a630c58625179053945ded1ae88aa Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 10:34:21 -0400
Subject: [PATCH 25/35] back out ubuntu to 22.04 for now to test - ga failing
 all of a sudden

---
 .github/workflows/main.yml | 2 +-
 poetry.lock                | 2 +-
 pyproject.toml             | 8 ++++----
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5ec18cdda..d9d6dd741 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,7 +20,7 @@ jobs:
     name: Test dcicutils with Python ${{ matrix.python_version }}
 
     # The type of runner that the job will run on
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         python_version: [3.8, 3.9, 3.11]
diff --git a/poetry.lock b/poetry.lock
index d7a42df51..ea0071db0 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1606,4 +1606,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "cf533f908fb4f451ada1932dfa17d6c47beb8052126bf286ee82a4fa3eb1cc65"
+content-hash = "6cdcf4e9fab04bbcaa83c3054b61356b4830b55c67e2a362dd1af635ae75a688"
diff --git a/pyproject.toml b/pyproject.toml
index 4597cbdb7..56c666321 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,8 +38,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.12"
-boto3 = "^1.28.56"
-botocore = "^1.31.56"
+boto3 = "^1.28.54"
+botocore = "^1.31.54"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.
 # This value is intentionally pinned and must not be changed casually.
 elasticsearch = "7.13.4"
@@ -63,8 +63,8 @@ tqdm = "^4.65.0"
 
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.28.56"
-botocore-stubs = "^1.31.56"
+boto3-stubs = "^1.28.54"
+botocore-stubs = "^1.31.54"
 coverage = ">=7.2.3"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023

From 25a4b5829ee6a935b324d741f8b3ae647812ce3c Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 10:38:57 -0400
Subject: [PATCH 26/35] put back update to ubuntu 20.04 -> 22.04 for ga and see
 if ga fails now

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d9d6dd741..5ec18cdda 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,7 +20,7 @@ jobs:
     name: Test dcicutils with Python ${{ matrix.python_version }}
 
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python_version: [3.8, 3.9, 3.11]

From 96cc528c1e620bb0a8b1b49a44f2f3f7075346bf Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 10:44:08 -0400
Subject: [PATCH 27/35] ga failed with ubuntu 22.04 for python 3.11 - put back
 20.04 to make sure it passes again

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5ec18cdda..d9d6dd741 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,7 +20,7 @@ jobs:
     name: Test dcicutils with Python ${{ matrix.python_version }}
 
     # The type of runner that the job will run on
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         python_version: [3.8, 3.9, 3.11]

From 97f1173700a3da101951f13b7678df12e19896fd Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 11:07:10 -0400
Subject: [PATCH 28/35] put ubuntu 22.04 back for ga and add testing hack in
 qa_utils.py

---
 .github/workflows/main.yml | 2 +-
 dcicutils/qa_utils.py      | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d9d6dd741..5ec18cdda 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -20,7 +20,7 @@ jobs:
     name: Test dcicutils with Python ${{ matrix.python_version }}
 
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python_version: [3.8, 3.9, 3.11]
diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py
index 8b440c413..c55a8b812 100644
--- a/dcicutils/qa_utils.py
+++ b/dcicutils/qa_utils.py
@@ -2308,6 +2308,7 @@ def get_object(self, Bucket, Key, **kwargs):  # noqa - Uppercase argument names
         "application/json": [".json"],
         "text/plain": [".txt", ".text"],
         "binary/octet-stream": [".fo"],
+        "application/vnd.software602.filler.form+xml": [".json"], # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28
     }
 
     def put_object(self, *, Bucket, Key, Body, ContentType=None, **kwargs):  # noqa - Uppercase argument names are chosen by AWS

From b226d61379d6f785d1f5a540b0069a20ade731fa Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 11:08:55 -0400
Subject: [PATCH 29/35] flake8 error

---
 dcicutils/qa_utils.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py
index c55a8b812..41f85aa7a 100644
--- a/dcicutils/qa_utils.py
+++ b/dcicutils/qa_utils.py
@@ -2308,7 +2308,8 @@ def get_object(self, Bucket, Key, **kwargs):  # noqa - Uppercase argument names
         "application/json": [".json"],
         "text/plain": [".txt", ".text"],
         "binary/octet-stream": [".fo"],
-        "application/vnd.software602.filler.form+xml": [".json"], # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28
+        # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 ...
+        "application/vnd.software602.filler.form+xml": [".json"],
     }
 
     def put_object(self, *, Bucket, Key, Body, ContentType=None, **kwargs):  # noqa - Uppercase argument names are chosen by AWS

From 45064b2f60487ec008cfaddd8c35a97b3ee79636 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 11:13:45 -0400
Subject: [PATCH 30/35] more hacking of qa_utils for troubleshooting ga failure
 with ubuntu 22.04

---
 dcicutils/qa_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py
index 41f85aa7a..42271fd54 100644
--- a/dcicutils/qa_utils.py
+++ b/dcicutils/qa_utils.py
@@ -2309,7 +2309,7 @@ def get_object(self, Bucket, Key, **kwargs):  # noqa - Uppercase argument names
         "text/plain": [".txt", ".text"],
         "binary/octet-stream": [".fo"],
         # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 ...
-        "application/vnd.software602.filler.form+xml": [".json"],
+        "application/vnd.software602.filler.form+xml": [".fo"],
     }
 
     def put_object(self, *, Bucket, Key, Body, ContentType=None, **kwargs):  # noqa - Uppercase argument names are chosen by AWS

From bd6a79748df638e8ce1f558b3b2362630ec043ed Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 12:02:10 -0400
Subject: [PATCH 31/35] Updated comments

---
 dcicutils/qa_utils.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py
index 42271fd54..0c9b019ed 100644
--- a/dcicutils/qa_utils.py
+++ b/dcicutils/qa_utils.py
@@ -2308,7 +2308,9 @@ def get_object(self, Bucket, Key, **kwargs):  # noqa - Uppercase argument names
         "application/json": [".json"],
         "text/plain": [".txt", ".text"],
         "binary/octet-stream": [".fo"],
-        # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 ...
+        # The below is because on Ubuntu 22.04 (docker), as opposed to 20.04, the mimetypes.guess_type
+        # function returns this strange value for an argument ending in ".fo"; this manifested as a test
+        # failure (put_object assert below) in test_s3_utils.test_unzip_s3_to_s3_unit. dmichaels/2023-09-28.
         "application/vnd.software602.filler.form+xml": [".fo"],
     }
 

From 96a10cb6189884221cc9fe218e836f3b765c50f4 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 28 Sep 2023 12:54:07 -0400
Subject: [PATCH 32/35] Fix to qa_utils for
 application/vnd.software602.filler.form+xml mime type return from
 mimetypes.guess_type on Ubuntu 22.04.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 56c666321..f87568801 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b8"  # TODO: To become 8.0.0
+version = "7.12.0.1b9"  # TODO: To become 8.0.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From f7c05b5d1aeaed68b8f747833b558a17e4d42954 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 29 Sep 2023 13:44:49 -0400
Subject: [PATCH 33/35] poetry update

---
 poetry.lock    | 163 +++++++++++++++++++++++--------------------------
 pyproject.toml |   8 +--
 2 files changed, 80 insertions(+), 91 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 471323aa3..ba5a1bb74 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -45,17 +45,17 @@ lxml = ["lxml"]
 
 [[package]]
 name = "boto3"
-version = "1.28.56"
+version = "1.28.57"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.56-py3-none-any.whl", hash = "sha256:f5fcb27cdbd08ca38d699f2d2e32d96d1d9fab3368c15c6bc326256612d2cfd7"},
-    {file = "boto3-1.28.56.tar.gz", hash = "sha256:b927a7ed335d543c33c15fa63f1076f3fa8422959771c2187da74bc4395ab6e3"},
+    {file = "boto3-1.28.57-py3-none-any.whl", hash = "sha256:5ddf24cf52c7fb6aaa332eaa08ae8c2afc8f2d1e8860680728533dd573904e32"},
+    {file = "boto3-1.28.57.tar.gz", hash = "sha256:e2d2824ba6459b330d097e94039a9c4f96ae3f4bcdc731d620589ad79dcd16d3"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.56,<1.32.0"
+botocore = ">=1.31.57,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.7.0,<0.8.0"
 
@@ -64,13 +64,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "boto3-stubs"
-version = "1.28.56"
-description = "Type annotations for boto3 1.28.56 generated with mypy-boto3-builder 7.19.0"
+version = "1.28.57"
+description = "Type annotations for boto3 1.28.57 generated with mypy-boto3-builder 7.19.0"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "boto3-stubs-1.28.56.tar.gz", hash = "sha256:2b77d4b9e944ffa4308822dc0327269f47cc4527a97903a3c5d14b9abed4eaad"},
-    {file = "boto3_stubs-1.28.56-py3-none-any.whl", hash = "sha256:e9c1f32463cf8e6ba56588f7c0f5cae52190b87eb19744ad1067a717be1c80b3"},
+    {file = "boto3-stubs-1.28.57.tar.gz", hash = "sha256:61cd792792c2a16d70801d187ebed705c39962a70e90b5dc0f33d04001fb39ae"},
+    {file = "boto3_stubs-1.28.57-py3-none-any.whl", hash = "sha256:b389a693e33d75ed19d38b4a2ba99d25f4f2045a3136f816d7fec4d27a71ddb4"},
 ]
 
 [package.dependencies]
@@ -84,7 +84,7 @@ account = ["mypy-boto3-account (>=1.28.0,<1.29.0)"]
 acm = ["mypy-boto3-acm (>=1.28.0,<1.29.0)"]
 acm-pca = ["mypy-boto3-acm-pca (>=1.28.0,<1.29.0)"]
 alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)"]
-all = ["mypy-boto3-accessanalyzer (>=1.28.0,<1.29.0)", "mypy-boto3-account (>=1.28.0,<1.29.0)", "mypy-boto3-acm (>=1.28.0,<1.29.0)", "mypy-boto3-acm-pca (>=1.28.0,<1.29.0)", "mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)", "mypy-boto3-amp (>=1.28.0,<1.29.0)", "mypy-boto3-amplify (>=1.28.0,<1.29.0)", "mypy-boto3-amplifybackend (>=1.28.0,<1.29.0)", "mypy-boto3-amplifyuibuilder (>=1.28.0,<1.29.0)", "mypy-boto3-apigateway (>=1.28.0,<1.29.0)", "mypy-boto3-apigatewaymanagementapi (>=1.28.0,<1.29.0)", "mypy-boto3-apigatewayv2 (>=1.28.0,<1.29.0)", "mypy-boto3-appconfig (>=1.28.0,<1.29.0)", "mypy-boto3-appconfigdata (>=1.28.0,<1.29.0)", "mypy-boto3-appfabric (>=1.28.0,<1.29.0)", "mypy-boto3-appflow (>=1.28.0,<1.29.0)", "mypy-boto3-appintegrations (>=1.28.0,<1.29.0)", "mypy-boto3-application-autoscaling (>=1.28.0,<1.29.0)", "mypy-boto3-application-insights (>=1.28.0,<1.29.0)", "mypy-boto3-applicationcostprofiler (>=1.28.0,<1.29.0)", "mypy-boto3-appmesh (>=1.28.0,<1.29.0)", "mypy-boto3-apprunner (>=1.28.0,<1.29.0)", "mypy-boto3-appstream (>=1.28.0,<1.29.0)", "mypy-boto3-appsync (>=1.28.0,<1.29.0)", "mypy-boto3-arc-zonal-shift (>=1.28.0,<1.29.0)", "mypy-boto3-athena (>=1.28.0,<1.29.0)", "mypy-boto3-auditmanager (>=1.28.0,<1.29.0)", "mypy-boto3-autoscaling (>=1.28.0,<1.29.0)", "mypy-boto3-autoscaling-plans (>=1.28.0,<1.29.0)", "mypy-boto3-backup (>=1.28.0,<1.29.0)", "mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)", "mypy-boto3-backupstorage (>=1.28.0,<1.29.0)", "mypy-boto3-batch (>=1.28.0,<1.29.0)", "mypy-boto3-billingconductor (>=1.28.0,<1.29.0)", "mypy-boto3-braket (>=1.28.0,<1.29.0)", "mypy-boto3-budgets (>=1.28.0,<1.29.0)", "mypy-boto3-ce (>=1.28.0,<1.29.0)", "mypy-boto3-chime (>=1.28.0,<1.29.0)", "mypy-boto3-chime-sdk-identity (>=1.28.0,<1.29.0)", "mypy-boto3-chime-sdk-media-pipelines (>=1.28.0,<1.29.0)", "mypy-boto3-chime-sdk-meetings (>=1.28.0,<1.29.0)", "mypy-boto3-chime-sdk-messaging (>=1.28.0,<1.29.0)", "mypy-boto3-chime-sdk-voice (>=1.28.0,<1.29.0)", "mypy-boto3-cleanrooms (>=1.28.0,<1.29.0)", "mypy-boto3-cloud9 (>=1.28.0,<1.29.0)", "mypy-boto3-cloudcontrol (>=1.28.0,<1.29.0)", "mypy-boto3-clouddirectory (>=1.28.0,<1.29.0)", "mypy-boto3-cloudformation (>=1.28.0,<1.29.0)", "mypy-boto3-cloudfront (>=1.28.0,<1.29.0)", "mypy-boto3-cloudhsm (>=1.28.0,<1.29.0)", "mypy-boto3-cloudhsmv2 (>=1.28.0,<1.29.0)", "mypy-boto3-cloudsearch (>=1.28.0,<1.29.0)", "mypy-boto3-cloudsearchdomain (>=1.28.0,<1.29.0)", "mypy-boto3-cloudtrail (>=1.28.0,<1.29.0)", "mypy-boto3-cloudtrail-data (>=1.28.0,<1.29.0)", "mypy-boto3-cloudwatch (>=1.28.0,<1.29.0)", "mypy-boto3-codeartifact (>=1.28.0,<1.29.0)", "mypy-boto3-codebuild (>=1.28.0,<1.29.0)", "mypy-boto3-codecatalyst (>=1.28.0,<1.29.0)", "mypy-boto3-codecommit (>=1.28.0,<1.29.0)", "mypy-boto3-codedeploy (>=1.28.0,<1.29.0)", "mypy-boto3-codeguru-reviewer (>=1.28.0,<1.29.0)", "mypy-boto3-codeguru-security (>=1.28.0,<1.29.0)", "mypy-boto3-codeguruprofiler (>=1.28.0,<1.29.0)", "mypy-boto3-codepipeline (>=1.28.0,<1.29.0)", "mypy-boto3-codestar (>=1.28.0,<1.29.0)", "mypy-boto3-codestar-connections (>=1.28.0,<1.29.0)", "mypy-boto3-codestar-notifications (>=1.28.0,<1.29.0)", "mypy-boto3-cognito-identity (>=1.28.0,<1.29.0)", "mypy-boto3-cognito-idp (>=1.28.0,<1.29.0)", "mypy-boto3-cognito-sync (>=1.28.0,<1.29.0)", "mypy-boto3-comprehend (>=1.28.0,<1.29.0)", "mypy-boto3-comprehendmedical (>=1.28.0,<1.29.0)", "mypy-boto3-compute-optimizer (>=1.28.0,<1.29.0)", "mypy-boto3-config (>=1.28.0,<1.29.0)", "mypy-boto3-connect (>=1.28.0,<1.29.0)", "mypy-boto3-connect-contact-lens (>=1.28.0,<1.29.0)", "mypy-boto3-connectcampaigns (>=1.28.0,<1.29.0)", "mypy-boto3-connectcases (>=1.28.0,<1.29.0)", "mypy-boto3-connectparticipant (>=1.28.0,<1.29.0)", "mypy-boto3-controltower (>=1.28.0,<1.29.0)", "mypy-boto3-cur (>=1.28.0,<1.29.0)", "mypy-boto3-customer-profiles (>=1.28.0,<1.29.0)", "mypy-boto3-databrew (>=1.28.0,<1.29.0)", "mypy-boto3-dataexchange (>=1.28.0,<1.29.0)", "mypy-boto3-datapipeline (>=1.28.0,<1.29.0)", "mypy-boto3-datasync (>=1.28.0,<1.29.0)", "mypy-boto3-dax (>=1.28.0,<1.29.0)", "mypy-boto3-detective (>=1.28.0,<1.29.0)", "mypy-boto3-devicefarm (>=1.28.0,<1.29.0)", "mypy-boto3-devops-guru (>=1.28.0,<1.29.0)", "mypy-boto3-directconnect (>=1.28.0,<1.29.0)", "mypy-boto3-discovery (>=1.28.0,<1.29.0)", "mypy-boto3-dlm (>=1.28.0,<1.29.0)", "mypy-boto3-dms (>=1.28.0,<1.29.0)", "mypy-boto3-docdb (>=1.28.0,<1.29.0)", "mypy-boto3-docdb-elastic (>=1.28.0,<1.29.0)", "mypy-boto3-drs (>=1.28.0,<1.29.0)", "mypy-boto3-ds (>=1.28.0,<1.29.0)", "mypy-boto3-dynamodb (>=1.28.0,<1.29.0)", "mypy-boto3-dynamodbstreams (>=1.28.0,<1.29.0)", "mypy-boto3-ebs (>=1.28.0,<1.29.0)", "mypy-boto3-ec2 (>=1.28.0,<1.29.0)", "mypy-boto3-ec2-instance-connect (>=1.28.0,<1.29.0)", "mypy-boto3-ecr (>=1.28.0,<1.29.0)", "mypy-boto3-ecr-public (>=1.28.0,<1.29.0)", "mypy-boto3-ecs (>=1.28.0,<1.29.0)", "mypy-boto3-efs (>=1.28.0,<1.29.0)", "mypy-boto3-eks (>=1.28.0,<1.29.0)", 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+    {file = "cffi-1.16.0.tar.gz", hash = "sha256:bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0"},
 ]
 
 [package.dependencies]
@@ -917,7 +907,6 @@ files = [
 name = "jsonc-parser"
 version = "1.1.5"
 description = "A lightweight, native tool for parsing .jsonc files"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1554,13 +1543,13 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.6"
+version = "0.2.7"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
 files = [
-    {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"},
-    {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"},
+    {file = "wcwidth-0.2.7-py2.py3-none-any.whl", hash = "sha256:fabf3e32999d9b0dab7d19d845149f326f04fe29bac67709ee071dbd92640a36"},
+    {file = "wcwidth-0.2.7.tar.gz", hash = "sha256:1b6d30a98ddd5ce9bbdb33658191fd2423fc9da203fe3ef1855407dcb7ee4e26"},
 ]
 
 [[package]]
@@ -1618,4 +1607,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "6cdcf4e9fab04bbcaa83c3054b61356b4830b55c67e2a362dd1af635ae75a688"
+content-hash = "cece532417080e22830d01f30a6589df2f8e94465896e57cd14e77ae91f89b4a"
diff --git a/pyproject.toml b/pyproject.toml
index 99c10d592..290713fe3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,8 +38,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.12"
-boto3 = "^1.28.54"
-botocore = "^1.31.54"
+boto3 = "^1.28.57"
+botocore = "^1.31.57"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.
 # This value is intentionally pinned and must not be changed casually.
 elasticsearch = "7.13.4"
@@ -64,8 +64,8 @@ tqdm = "^4.65.0"
 
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.28.54"
-botocore-stubs = "^1.31.54"
+boto3-stubs = "^1.28.57"
+botocore-stubs = "^1.31.57"
 coverage = ">=7.2.3"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023

From 27e11b6a08750036ec0c905a0ef3d5d5618e41ae Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 29 Sep 2023 13:59:41 -0400
Subject: [PATCH 34/35] Bumped to Python 3.11 in static-checks.yml

---
 .github/workflows/static-checks.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/static-checks.yml b/.github/workflows/static-checks.yml
index 0d914f264..aa2a095b6 100644
--- a/.github/workflows/static-checks.yml
+++ b/.github/workflows/static-checks.yml
@@ -27,7 +27,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Python Package Setup
         run: |
           make configure

From 2699a4da5a203b49abf88187a9eb8901297dd91e Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 5 Oct 2023 12:25:26 -0400
Subject: [PATCH 35/35] Update version to 8.0.0; ready to merge to master.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 290713fe3..804de6f74 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "7.12.0.1b10"  # TODO: To become 8.0.0
+version = "8.0.0"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"