From d081fff53594243a0f39b84fc702d38c493553e7 Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 13 Dec 2023 12:52:21 -0700
Subject: [PATCH] relax sssom constraints

---
 poetry.lock    | 381 ++++++++++++++++++++++++++-----------------------
 pyproject.toml |   4 +-
 2 files changed, 205 insertions(+), 180 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d68a42d..fc4d40b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -60,18 +60,15 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 
 [[package]]
 name = "babel"
-version = "2.13.1"
+version = "2.14.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
-    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
 ]
 
-[package.dependencies]
-setuptools = {version = "*", markers = "python_version >= \"3.12\""}
-
 [package.extras]
 dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
@@ -111,29 +108,33 @@ prefixmaps = "*"
 
 [[package]]
 name = "black"
-version = "23.11.0"
+version = "23.12.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "black-23.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:81a832b6e00eef2c13b3239d514ea3b7d5cc3eaa03d0474eedcbbda59441ba5d"},
+    {file = "black-23.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:6a82a711d13e61840fb11a6dfecc7287f2424f1ca34765e70c909a35ffa7fb95"},
+    {file = "black-23.12.0-py3-none-any.whl", hash = "sha256:a7c07db8200b5315dc07e331dda4d889a56f6bf4db6a9c2a526fa3166a81614f"},
+    {file = "black-23.12.0.tar.gz", hash = "sha256:330a327b422aca0634ecd115985c1c7fd7bdb5b5a2ef8aa9888a82e2ebe9437a"},
 ]
 
 [package.dependencies]
@@ -147,7 +148,7 @@ typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
+d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
@@ -358,13 +359,13 @@ tests = ["coverage", "pytest"]
 
 [[package]]
 name = "dask"
-version = "2023.11.0"
+version = "2023.12.0"
 description = "Parallel PyData with Task Scheduling"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "dask-2023.11.0-py3-none-any.whl", hash = "sha256:b950951ee3f8c86f003b577b6928ecf20089eee6677719578deaba8fd9a78203"},
-    {file = "dask-2023.11.0.tar.gz", hash = "sha256:06b8f39755d37ff6ef4db422774db1f1d5d6788d33f0628c80861dc6452f878c"},
+    {file = "dask-2023.12.0-py3-none-any.whl", hash = "sha256:6cef2fa43815adc8fe895dd3ea473a311249ba0e15e1f7eb9b1b68302339d998"},
+    {file = "dask-2023.12.0.tar.gz", hash = "sha256:3f687e647ced0d3f2cadbef113c730b6555b9499b62e3a220535438841001c91"},
 ]
 
 [package.dependencies]
@@ -382,7 +383,7 @@ array = ["numpy (>=1.21)"]
 complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)", "pyarrow-hotfix"]
 dataframe = ["dask[array]", "pandas (>=1.3)"]
 diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
-distributed = ["distributed (==2023.11.0)"]
+distributed = ["distributed (==2023.12.0)"]
 test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
 
 [[package]]
@@ -418,13 +419,13 @@ packaging = "*"
 
 [[package]]
 name = "distlib"
-version = "0.3.7"
+version = "0.3.8"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
 files = [
-    {file = "distlib-0.3.7-py2.py3-none-any.whl", hash = "sha256:2e24928bc811348f0feb63014e97aaae3037f2cf48712d51ae61df7fd6075057"},
-    {file = "distlib-0.3.7.tar.gz", hash = "sha256:9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8"},
+    {file = "distlib-0.3.8-py2.py3-none-any.whl", hash = "sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784"},
+    {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"},
 ]
 
 [[package]]
@@ -492,13 +493,13 @@ files = [
 
 [[package]]
 name = "fsspec"
-version = "2023.10.0"
+version = "2023.12.2"
 description = "File-system specification"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "fsspec-2023.10.0-py3-none-any.whl", hash = "sha256:346a8f024efeb749d2a5fca7ba8854474b1ff9af7c3faaf636a4548781136529"},
-    {file = "fsspec-2023.10.0.tar.gz", hash = "sha256:330c66757591df346ad3091a53bd907e15348c2ba17d63fd54f5c39c4457d2a5"},
+    {file = "fsspec-2023.12.2-py3-none-any.whl", hash = "sha256:d800d87f72189a745fa3d6b033b9dc4a34ad069f60ca60b943a63599f5501960"},
+    {file = "fsspec-2023.12.2.tar.gz", hash = "sha256:8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb"},
 ]
 
 [package.extras]
@@ -560,68 +561,69 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=
 
 [[package]]
 name = "greenlet"
-version = "3.0.1"
+version = "3.0.2"
 description = "Lightweight in-process concurrent programming"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -630,13 +632,13 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "griffe"
-version = "0.38.0"
+version = "0.38.1"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -666,20 +668,20 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "7.0.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
 testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
@@ -877,13 +879,13 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "linkml"
-version = "1.6.3"
+version = "1.6.5"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = ">=3.8.1,<4.0.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1131,13 +1133,13 @@ mkdocs = ">=1.1"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.4.14"
+version = "9.5.2"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1359,36 +1361,36 @@ files = [
 
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 name = "pandas"
-version = "2.1.3"
+version = "2.1.4"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "pandas-2.1.4.tar.gz", hash = "sha256:fcb68203c833cc735321512e13861358079a96c174a61f5116a1de89c58c0ef7"},
 ]
 
 [package.dependencies]
@@ -1472,24 +1474,24 @@ complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"]
 
 [[package]]
 name = "pathspec"
-version = "0.11.2"
+version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "platformdirs"
-version = "4.0.0"
+version = "4.1.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2017,13 +2019,13 @@ rdflib-jsonld = "0.6.1"
 
 [[package]]
 name = "referencing"
-version = "0.31.1"
+version = "0.32.0"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2309,30 +2311,50 @@ files = [
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@@ -2601,24 +2627,23 @@ sqlcipher = ["sqlcipher3-binary"]
 
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 name = "sssom"
-version = "0.3.41"
+version = "0.4.2"
 description = "Operations on SSSOM mapping tables"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
-    {file = "sssom-0.3.41-py3-none-any.whl", hash = "sha256:04ce1935b3492019b16b7b748c49af366f84bbd3c059982af992d049f46098e7"},
-    {file = "sssom-0.3.41.tar.gz", hash = "sha256:1d09fa9f88153963372811af829ebc1e5aefff935a4e6e12bcb65c94181aa730"},
+    {file = "sssom-0.4.2-py3-none-any.whl", hash = "sha256:4ca51db9c22c9f946fb002f23b9260906f6024799ddea556a1612a3495c3b480"},
+    {file = "sssom-0.4.2.tar.gz", hash = "sha256:19c8788573221e63ca092c9d2ffb0a3e88834901cd8b7fedad07e6ad26ef5d49"},
 ]
 
 [package.dependencies]
 click = ">=8.1.6"
-curies = ">=0.5.7"
+curies = ">=0.7.3"
 deprecation = ">=2.1.0,<3.0.0"
-importlib-metadata = ">=6.8.0"
 linkml-runtime = ">=1.5.5"
-networkx = ">=3.1"
-pandas = ">=2.0.3"
-pansql = ">=0.0.1"
+networkx = {version = ">=3.1", extras = ["networkx"]}
+pandas = ">1.0.3"
+pansql = {version = ">=0.0.1", extras = ["pansql"]}
 pyyaml = ">=6.0.1,<7.0.0"
 rdflib = ">=6.0.0"
 scipy = {version = "*", extras = ["scipy"]}
@@ -2739,13 +2764,13 @@ files = [
 
 [[package]]
 name = "typing-extensions"
-version = "4.8.0"
+version = "4.9.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
-    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+    {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
+    {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
 ]
 
 [[package]]
@@ -2813,13 +2838,13 @@ tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4
 
 [[package]]
 name = "virtualenv"
-version = "20.24.7"
+version = "20.25.0"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "virtualenv-20.24.7-py3-none-any.whl", hash = "sha256:a18b3fd0314ca59a2e9f4b556819ed07183b3e9a3702ecfe213f593d44f7b3fd"},
-    {file = "virtualenv-20.24.7.tar.gz", hash = "sha256:69050ffb42419c91f6c1284a7b24e0475d793447e35929b488bf6a0aade39353"},
+    {file = "virtualenv-20.25.0-py3-none-any.whl", hash = "sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3"},
+    {file = "virtualenv-20.25.0.tar.gz", hash = "sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b"},
 ]
 
 [package.dependencies]
@@ -2996,4 +3021,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "483968ebd2b81ffaf58a51a968913086e3a31d8ff0dd70ad36d1a99b639da2d3"
+content-hash = "24fcafa107fbce6d07560a3b1895b472ff9a02247554c830850e0d313f516491"
diff --git a/pyproject.toml b/pyproject.toml
index a3699a6..b521cb8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "koza"
-version = "0.5.2"
+version = "0.5.3"
 description = "Data transformation framework for LinkML data models"
 authors = [
     "The Monarch Initiative <info@monarchinitiative.org>",
@@ -24,7 +24,7 @@ ordered-set = ">=4.1.0"
 typer = "^0.7.0"
 typer-cli = "^0.0.13"
 loguru = "*"
-sssom = "^0.3.41"
+sssom = ">=0.4"
 
 [tool.poetry.dev-dependencies]
 black = "^23.10.0"