diff --git a/.cruft.json b/.cruft.json
index f63bdeb..57d6ee3 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/monarch-initiative/monarch-project-template/",
-  "commit": "0fce395fe859618d3feb3ac9ebd2f8b94d743b2b",
+  "commit": "e5f758215fa58b92093e71b632f804569fde9dba",
   "checkout": null,
   "context": {
     "cookiecutter": {
diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
index 1029d9c..b25530d 100644
--- a/.github/workflows/deploy-docs.yml
+++ b/.github/workflows/deploy-docs.yml
@@ -10,7 +10,7 @@ jobs:
       uses: actions/checkout@v3.0.2
       with:
         fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-    
+
     - name: Set up Python 3.
       uses: actions/setup-python@v3
       with:
@@ -21,8 +21,8 @@ jobs:
 
     - name: Install dependencies.
       run: |
-        poetry install -E docs
-        
+        poetry install --with docs
+
     - name: Build documentation.
       run: |
         echo ${{ secrets.GH_TOKEN }} >> src/curate_gpt/token.txt
@@ -31,8 +31,8 @@ jobs:
         cd docs/
         poetry run sphinx-apidoc -o . ../src/curate_gpt/ --ext-autodoc -f
         poetry run sphinx-build -b html . _build
-        cp -r _build/html/* ../gh-pages/
-    
+        cp -r _build/* ../gh-pages/
+
     - name: Deploy documentation.
       if: ${{ github.event_name == 'push' }}
       uses: JamesIves/github-pages-deploy-action@v4.4.1
diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
index e100f1f..c2c1d5e 100644
--- a/.github/workflows/pypi-publish.yml
+++ b/.github/workflows/pypi-publish.yml
@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
   release:
     types: [created]
-    
+
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI
@@ -20,7 +20,7 @@ jobs:
 
       - name: Install Poetry
         run: pip install poetry poetry-dynamic-versioning
-    
+
       - name: Install dependencies
         run: poetry install --no-interaction
 
@@ -32,5 +32,3 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
-
-    
\ No newline at end of file
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
index 126bbaf..5dbe194 100644
--- a/.github/workflows/qc.yml
+++ b/.github/workflows/qc.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: [ "3.8", "3.11" ]
 
     steps:
       - uses: actions/checkout@v3.0.2
@@ -26,8 +26,11 @@ jobs:
       - name: Install dependencies
         run: poetry install --no-interaction
 
+      - name: Check common spelling errors
+        run: poetry run tox -e codespell
+
       - name: Check code quality with flake8
-        run: poetry run tox -e flake8
+        run: poetry run tox -e lint
 
       - name: Test with pytest and generate coverage file
         run: poetry run tox -e py
diff --git a/.gitignore b/.gitignore
index 29bc2ec..a8f9868 100644
--- a/.gitignore
+++ b/.gitignore
@@ -135,4 +135,8 @@ dmypy.json
 .pyre/
 
 # User defined
-stagedb/*
\ No newline at end of file
+!tests/input/dbs/go-nucleus-chroma/*.sqlite3
+stagedb/*
+*.rej
+tests/input/dbs/go-nucleus-chroma/*/*.bin
+tests/output/*
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..b2e58a4
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,25 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-toml
+  - id: trailing-whitespace
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.278
+  hooks:
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix]
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+    additional_dependencies:
+      - tomli
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b17a899..64bc50e 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -29,4 +29,24 @@ Note: All the development must be done on a branch on your fork.
 
 ALSO NOTE: github.com lets you create a pull request from the main branch, automating the steps above.
 
-> A code review (which happens with both the contributor and the reviewer present) is required for contributing.
\ No newline at end of file
+> A code review (which happens with both the contributor and the reviewer present) is required for contributing.
+
+### How to write a great issue
+
+Please review GitHub's overview article,
+["Tracking Your Work with Issues"][about-issues].
+
+<a id="great-pulls"></a>
+
+### How to create a great pull/merge request
+
+Please review GitHub's article, ["About Pull Requests"][about-pulls],
+and make your changes on a [new branch][about-branches].
+
+[about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches
+[about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues
+[about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
+[issues]: https://github.com/monarch-initiative/curate-gpt/issues/
+[pulls]: https://github.com/monarch-initiative/curate-gpt/pulls/
+
+We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)
diff --git a/docs/conf.py b/docs/conf.py
index 380bd68..80e017d 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,5 +1,4 @@
-# Configuration file for the Sphinx documentation builder.
-#
+"""Configuration file for the Sphinx documentation builder."""
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
@@ -47,13 +46,13 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
diff --git a/poetry.lock b/poetry.lock
index f6c9c2e..fc516dc 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,119 +1,105 @@
-# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "aiohttp"
-version = "3.8.5"
+version = "3.9.1"
 description = "Async http client/server framework (asyncio)"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
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+    {file = "aiohttp-3.9.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:0d406b01a9f5a7e232d1b0d161b40c05275ffbcbd772dc18c1d5a570961a1ca4"},
+    {file = "aiohttp-3.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8d8e4450e7fe24d86e86b23cc209e0023177b6d59502e33807b732d2deb6975f"},
+    {file = "aiohttp-3.9.1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:3c0266cd6f005e99f3f51e583012de2778e65af6b73860038b968a0a8888487a"},
+    {file = "aiohttp-3.9.1-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:ab221850108a4a063c5b8a70f00dd7a1975e5a1713f87f4ab26a46e5feac5a0e"},
+    {file = "aiohttp-3.9.1-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:c88a15f272a0ad3d7773cf3a37cc7b7d077cbfc8e331675cf1346e849d97a4e5"},
+    {file = "aiohttp-3.9.1-cp39-cp39-musllinux_1_1_ppc64le.whl", hash = "sha256:237533179d9747080bcaad4d02083ce295c0d2eab3e9e8ce103411a4312991a0"},
+    {file = "aiohttp-3.9.1-cp39-cp39-musllinux_1_1_s390x.whl", hash = "sha256:02ab6006ec3c3463b528374c4cdce86434e7b89ad355e7bf29e2f16b46c7dd6f"},
+    {file = "aiohttp-3.9.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04fa38875e53eb7e354ece1607b1d2fdee2d175ea4e4d745f6ec9f751fe20c7c"},
+    {file = "aiohttp-3.9.1-cp39-cp39-win32.whl", hash = "sha256:82eefaf1a996060602f3cc1112d93ba8b201dbf5d8fd9611227de2003dddb3b7"},
+    {file = "aiohttp-3.9.1-cp39-cp39-win_amd64.whl", hash = "sha256:9b05d33ff8e6b269e30a7957bd3244ffbce2a7a35a81b81c382629b80af1a8bf"},
+    {file = "aiohttp-3.9.1.tar.gz", hash = "sha256:8fc49a87ac269d4529da45871e2ffb6874e87779c3d0e2ccd813c0899221239d"},
 ]
 
 [package.dependencies]
 aiosignal = ">=1.1.2"
-async-timeout = ">=4.0.0a3,<5.0"
+async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
-charset-normalizer = ">=2.0,<4.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
 yarl = ">=1.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli", "aiodns", "cchardet"]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
 
 [[package]]
 name = "aiosignal"
 version = "1.3.1"
 description = "aiosignal: a list of registered asynchronous callbacks"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -126,25 +112,23 @@ frozenlist = ">=1.1.0"
 
 [[package]]
 name = "airium"
-version = "0.2.5"
+version = "0.2.6"
 description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "airium-0.2.5-py3-none-any.whl", hash = "sha256:6b4d75a2ff1aca0d9f787bcd3a69df13a189a75806b2fa2c9acda2e30f0ef5be"},
-    {file = "airium-0.2.5.tar.gz", hash = "sha256:39a715fee1f6d81a75c31efa62bd13915d8648ea03937adf1ac07a6065f7cbec"},
+    {file = "airium-0.2.6-py3-none-any.whl", hash = "sha256:50af5cf491e084f27909e29a93550b4170e587cde01334d58c6249644ee8c6c2"},
+    {file = "airium-0.2.6.tar.gz", hash = "sha256:ccab36b798b6cce3d0c5074e52ce8059f6e82991caae4985f42cadfad80b1de4"},
 ]
 
 [package.extras]
-dev = ["pdbpp (>=0.10,<1.0)", "pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)"]
-parse = ["beautifulsoup4 (>=4.10,<5.0)", "requests (>=2.12,<3)"]
+dev = ["pytest (>=6.2,<7.0)", "pytest-cov (>=3.0,<4.0)", "pytest-mock (>=3.6,<4.0)"]
+parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"]
 
 [[package]]
 name = "alabaster"
 version = "0.7.13"
 description = "A configurable sidebar-enabled Sphinx theme"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -154,33 +138,41 @@ files = [
 
 [[package]]
 name = "altair"
-version = "5.0.1"
-description = "Vega-Altair: A declarative statistical visualization library for Python."
-category = "main"
+version = "4.2.2"
+description = "Altair: A declarative statistical visualization library for Python."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "altair-5.0.1-py3-none-any.whl", hash = "sha256:9f3552ed5497d4dfc14cf48a76141d8c29ee56eae2873481b4b28134268c9bbe"},
-    {file = "altair-5.0.1.tar.gz", hash = "sha256:087d7033cb2d6c228493a053e12613058a5d47faf6a36aea3ff60305fd8b4cb0"},
+    {file = "altair-4.2.2-py3-none-any.whl", hash = "sha256:8b45ebeaf8557f2d760c5c77b79f02ae12aee7c46c27c06014febab6f849bc87"},
+    {file = "altair-4.2.2.tar.gz", hash = "sha256:39399a267c49b30d102c10411e67ab26374156a84b1aeb9fcd15140429ba49c5"},
 ]
 
 [package.dependencies]
+entrypoints = "*"
 jinja2 = "*"
 jsonschema = ">=3.0"
 numpy = "*"
 pandas = ">=0.18"
 toolz = "*"
-typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-dev = ["black (<24)", "hatch", "ipython", "m2r", "mypy", "pandas-stubs", "pytest", "pytest-cov", "ruff", "types-jsonschema", "types-setuptools", "vega-datasets", "vl-convert-python"]
-doc = ["docutils", "geopandas", "jinja2", "myst-parser", "numpydoc", "pillow", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinxext-altair"]
+dev = ["black", "docutils", "flake8", "ipython", "m2r", "mistune (<2.0.0)", "pytest", "recommonmark", "sphinx", "vega-datasets"]
+
+[[package]]
+name = "annotated-types"
+version = "0.6.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
+    {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
+]
 
 [[package]]
 name = "antlr4-python3-runtime"
 version = "4.9.3"
 description = "ANTLR 4.9.3 runtime for Python 3.7"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -191,7 +183,6 @@ files = [
 name = "anyio"
 version = "3.7.1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -213,7 +204,6 @@ trio = ["trio (<0.22)"]
 name = "appdirs"
 version = "1.4.4"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -225,7 +215,6 @@ files = [
 name = "appnope"
 version = "0.1.3"
 description = "Disable App Nap on macOS >= 10.9"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -235,14 +224,13 @@ files = [
 
 [[package]]
 name = "argcomplete"
-version = "3.1.1"
+version = "3.1.6"
 description = "Bash tab completion for argparse"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "argcomplete-3.1.1-py3-none-any.whl", hash = "sha256:35fa893a88deea85ea7b20d241100e64516d6af6d7b0ae2bed1d263d26f70948"},
-    {file = "argcomplete-3.1.1.tar.gz", hash = "sha256:6c4c563f14f01440aaffa3eae13441c5db2357b5eec639abe7c0b15334627dff"},
+    {file = "argcomplete-3.1.6-py3-none-any.whl", hash = "sha256:71f4683bc9e6b0be85f2b2c1224c47680f210903e23512cfebfe5a41edfd883a"},
+    {file = "argcomplete-3.1.6.tar.gz", hash = "sha256:3b1f07d133332547a53c79437527c00be48cca3807b1d4ca5cab1b26313386a6"},
 ]
 
 [package.extras]
@@ -252,7 +240,6 @@ test = ["coverage", "mypy", "pexpect", "ruff", "wheel"]
 name = "argon2-cffi"
 version = "23.1.0"
 description = "Argon2 for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -273,7 +260,6 @@ typing = ["mypy"]
 name = "argon2-cffi-bindings"
 version = "21.2.0"
 description = "Low-level CFFI bindings for Argon2"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -309,42 +295,45 @@ tests = ["pytest"]
 
 [[package]]
 name = "arrow"
-version = "1.2.3"
+version = "1.3.0"
 description = "Better dates & times for Python"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"},
-    {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"},
+    {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
+    {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
 ]
 
 [package.dependencies]
 python-dateutil = ">=2.7.0"
+types-python-dateutil = ">=2.8.10"
+
+[package.extras]
+doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
 
 [[package]]
 name = "asttokens"
-version = "2.2.1"
+version = "2.4.1"
 description = "Annotate AST trees with source code positions"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "asttokens-2.2.1-py2.py3-none-any.whl", hash = "sha256:6b0ac9e93fb0335014d382b8fa9b3afa7df546984258005da0b9e7095b3deb1c"},
-    {file = "asttokens-2.2.1.tar.gz", hash = "sha256:4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3"},
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
 ]
 
 [package.dependencies]
-six = "*"
+six = ">=1.12.0"
 
 [package.extras]
-test = ["astroid", "pytest"]
+astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
+test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "async-lru"
 version = "2.0.4"
 description = "Simple LRU cache for asyncio"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -359,7 +348,6 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 name = "async-timeout"
 version = "4.0.3"
 description = "Timeout context manager for asyncio programs"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -371,7 +359,6 @@ files = [
 name = "attrs"
 version = "23.1.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -388,33 +375,25 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
 
 [[package]]
 name = "babel"
-version = "2.12.1"
+version = "2.13.1"
 description = "Internationalization utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
-    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
+    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
 ]
 
-[[package]]
-name = "backcall"
-version = "0.2.0"
-description = "Specifications for callback functions passed in to an API"
-category = "dev"
-optional = false
-python-versions = "*"
-files = [
-    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
-    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
-]
+[package.dependencies]
+setuptools = {version = "*", markers = "python_version >= \"3.12\""}
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "backoff"
 version = "2.2.1"
 description = "Function decoration for backoff and retry"
-category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -426,7 +405,6 @@ files = [
 name = "bcp47"
 version = "0.0.4"
 description = "Language tags made easy"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -436,33 +414,28 @@ files = [
 
 [[package]]
 name = "bcrypt"
-version = "4.0.1"
+version = "4.1.1"
 description = "Modern password hashing for your software and your servers"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "bcrypt-4.0.1-cp36-abi3-macosx_10_10_universal2.whl", hash = "sha256:b1023030aec778185a6c16cf70f359cbb6e0c289fd564a7cfa29e727a1c38f8f"},
-    {file = "bcrypt-4.0.1-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl", hash = "sha256:08d2947c490093a11416df18043c27abe3921558d2c03e2076ccb28a116cb6d0"},
-    {file = "bcrypt-4.0.1-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0eaa47d4661c326bfc9d08d16debbc4edf78778e6aaba29c1bc7ce67214d4410"},
-    {file = "bcrypt-4.0.1-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ae88eca3024bb34bb3430f964beab71226e761f51b912de5133470b649d82344"},
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 ]
 
 [package.extras]
@@ -473,7 +446,6 @@ typecheck = ["mypy"]
 name = "beautifulsoup4"
 version = "4.12.2"
 description = "Screen-scraping library"
-category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -490,13 +462,12 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bibtexparser"
-version = "1.4.0"
+version = "1.4.1"
 description = "Bibtex parser for python 3"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -506,7 +477,6 @@ pyparsing = ">=2.0.3"
 name = "bioc"
 version = "2.1"
 description = "bioc - Processing BioC, Brat, and PubTator with Python."
-category = "main"
 optional = true
 python-versions = ">=3.6"
 files = [
@@ -523,14 +493,13 @@ tqdm = "*"
 
 [[package]]
 name = "bleach"
-version = "6.0.0"
+version = "6.1.0"
 description = "An easy safelist-based HTML-sanitizing tool."
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -538,142 +507,125 @@ six = ">=1.9.0"
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.2)"]
+css = ["tinycss2 (>=1.1.0,<1.3)"]
 
 [[package]]
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+version = "1.7.0"
 description = "Fast, simple object-to-object and broadcast signaling"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "cachetools"
-version = "5.3.1"
+version = "5.3.2"
 description = "Extensible memoizing collections and decorators"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
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+version = "23.2.3"
 description = "Composable complex class support for attrs and dataclasses."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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-exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
-typing_extensions = {version = ">=4.1.0", markers = "python_version < \"3.11\""}
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+typing-extensions = {version = ">=4.1.0,<4.6.3 || >4.6.3", markers = "python_version < \"3.11\""}
 
 [package.extras]
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+msgpack = ["msgpack (>=1.0.5)"]
+orjson = ["orjson (>=3.9.2)"]
+pyyaml = ["pyyaml (>=6.0)"]
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+ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
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+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
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 [package.dependencies]
@@ -683,7 +635,6 @@ pycparser = "*"
 name = "cfgraph"
 version = "0.2.1"
 description = "rdflib collections flattening graph"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -697,7 +648,6 @@ rdflib = ">=0.4.2"
 name = "chardet"
 version = "5.2.0"
 description = "Universal encoding detector for Python 3"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -707,94 +657,107 @@ files = [
 
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 optional = false
 python-versions = ">=3.7.0"
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 ]
 
 [[package]]
 name = "chroma-hnswlib"
 version = "0.7.3"
 description = "Chromas fork of hnswlib"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -832,7 +795,6 @@ numpy = "*"
 name = "chromadb"
 version = "0.4.17"
 description = "Chroma."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -870,7 +832,6 @@ uvicorn = {version = ">=0.18.3", extras = ["standard"]}
 name = "class-resolver"
 version = "0.4.2"
 description = "Lookup and instantiate classes with style."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -897,7 +858,6 @@ torch-geometric = ["torch", "torch-geometric", "torch-sparse"]
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -912,7 +872,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "click-default-group"
 version = "1.2.4"
 description = "click_default_group"
-category = "main"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -926,26 +885,10 @@ click = "*"
 [package.extras]
 test = ["pytest"]
 
-[[package]]
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-
-[package.dependencies]
-click = "*"
-
 [[package]]
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 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -957,7 +900,6 @@ files = [
 name = "coloredlogs"
 version = "15.0.1"
 description = "Colored terminal output for Python's logging module"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -973,118 +915,114 @@ cron = ["capturer (>=2.4)"]
 
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 ]
 
 [package.dependencies]
 traitlets = ">=4"
 
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 test = ["pytest"]
-typing = ["mypy (>=0.990)"]
 
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 description = "Python library for calculating contours of 2D quadrilateral grids"
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 optional = false
-python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -1100,28 +1038,15 @@ ssh = ["bcrypt (>=3.1.5)"]
 test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
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 [[package]]
 name = "curies"
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 description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1139,49 +1064,50 @@ tests = ["coverage", "pytest"]
 
 [[package]]
 name = "cycler"
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+version = "0.12.1"
 description = "Composable style cycles"
-category = "main"
 optional = false
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 ]
 
+[package.extras]
+docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
+tests = ["pytest", "pytest-cov", "pytest-xdist"]
+
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 [[package]]
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1193,7 +1119,6 @@ files = [
 name = "defusedxml"
 version = "0.7.1"
 description = "XML bomb protection for Python stdlib modules"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -1205,7 +1130,6 @@ files = [
 name = "deprecated"
 version = "1.2.14"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1223,7 +1147,6 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 name = "deprecation"
 version = "2.1.0"
 description = "A library to handle automated deprecations"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1238,7 +1161,6 @@ packaging = "*"
 name = "distlib"
 version = "0.3.7"
 description = "Distribution utilities"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1250,7 +1172,6 @@ files = [
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 version = "2.4.2"
 description = "DNS toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -1270,7 +1191,6 @@ wmi = ["wmi (>=1.5.1,<2.0.0)"]
 name = "docopt"
 version = "0.6.2"
 description = "Pythonic argument parser, that will make you smile"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -1279,21 +1199,19 @@ files = [
 
 [[package]]
 name = "docutils"
-version = "0.18.1"
+version = "0.20.1"
 description = "Docutils -- Python Documentation Utilities"
-category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7"
 files = [
-    {file = "docutils-0.18.1-py2.py3-none-any.whl", hash = "sha256:23010f129180089fbcd3bc08cfefccb3b890b0050e1ca00c867036e9d161b98c"},
-    {file = "docutils-0.18.1.tar.gz", hash = "sha256:679987caf361a7539d76e584cbeddc311e3aee937877c87346f31debc63e9d06"},
+    {file = "docutils-0.20.1-py3-none-any.whl", hash = "sha256:96f387a2c5562db4476f09f13bbab2192e764cac08ebbf3a34a95d9b1e4a59d6"},
+    {file = "docutils-0.20.1.tar.gz", hash = "sha256:f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b"},
 ]
 
 [[package]]
 name = "docx2txt"
 version = "0.8"
 description = "A pure python-based utility to extract text and images from docx files."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1304,7 +1222,6 @@ files = [
 name = "ebooklib"
 version = "0.18"
 description = "Ebook library which can handle EPUB2/EPUB3 and Kindle format"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1319,7 +1236,6 @@ six = "*"
 name = "editorconfig"
 version = "0.12.3"
 description = "EditorConfig File Locator and Interpreter for Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1327,11 +1243,21 @@ files = [
     {file = "EditorConfig-0.12.3.tar.gz", hash = "sha256:57f8ce78afcba15c8b18d46b5170848c88d56fd38f05c2ec60dbbfcb8996e89e"},
 ]
 
+[[package]]
+name = "entrypoints"
+version = "0.4"
+description = "Discover and load entry points from installed packages."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "entrypoints-0.4-py3-none-any.whl", hash = "sha256:f174b5ff827504fd3cd97cc3f8649f3693f51538c7e4bdf3ef002c8429d42f9f"},
+    {file = "entrypoints-0.4.tar.gz", hash = "sha256:b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4"},
+]
+
 [[package]]
 name = "et-xmlfile"
 version = "1.1.0"
 description = "An implementation of lxml.xmlfile for the standard library"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1343,7 +1269,6 @@ files = [
 name = "eutils"
 version = "0.6.0"
 description = "\"Python interface to NCBI's eutilities API\""
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1361,14 +1286,13 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.3"
+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"},
-    {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"},
+    {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
+    {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
 ]
 
 [package.extras]
@@ -1376,29 +1300,27 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "executing"
-version = "1.2.0"
+version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
-category = "dev"
 optional = false
-python-versions = "*"
+python-versions = ">=3.5"
 files = [
-    {file = "executing-1.2.0-py2.py3-none-any.whl", hash = "sha256:0314a69e37426e3608aada02473b4161d4caf5a4b244d1d0c48072b8fee7bacc"},
-    {file = "executing-1.2.0.tar.gz", hash = "sha256:19da64c18d2d851112f09c287f8d3dbbdf725ab0e569077efb6cdcbd3497c107"},
+    {file = "executing-2.0.1-py2.py3-none-any.whl", hash = "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"},
+    {file = "executing-2.0.1.tar.gz", hash = "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147"},
 ]
 
 [package.extras]
-tests = ["asttokens", "littleutils", "pytest", "rich"]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
 
 [[package]]
 name = "fake-useragent"
-version = "1.2.1"
+version = "1.4.0"
 description = "Up-to-date simple useragent faker with real world database"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "fake-useragent-1.2.1.tar.gz", hash = "sha256:b411f903331f695e3840ccadcf011f745a405764e97c588f2b8fde9e400a5446"},
-    {file = "fake_useragent-1.2.1-py3-none-any.whl", hash = "sha256:ad2b5414d19493d0789572f04200d4f656f84d20b205cc805233212957fe385d"},
+    {file = "fake-useragent-1.4.0.tar.gz", hash = "sha256:5426e4015d8ccc5bb25f64d3dfcfd3915eba30ffebd31b86b60dc7a4c5d65528"},
+    {file = "fake_useragent-1.4.0-py3-none-any.whl", hash = "sha256:9acce439ee2c6cf9c3772fa6c200f62dc8d56605063327a4d8c5d0e47f414b85"},
 ]
 
 [package.dependencies]
@@ -1406,34 +1328,33 @@ importlib-resources = {version = ">=5.0", markers = "python_version < \"3.10\""}
 
 [[package]]
 name = "fastapi"
-version = "0.99.1"
+version = "0.104.1"
 description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "fastapi-0.99.1-py3-none-any.whl", hash = "sha256:976df7bab51ac7beda9f68c4513b8c4490b5c1135c72aafd0a5ee4023ec5282e"},
-    {file = "fastapi-0.99.1.tar.gz", hash = "sha256:ac78f717cd80d657bd183f94d33b9bda84aa376a46a9dab513586b8eef1dc6fc"},
+    {file = "fastapi-0.104.1-py3-none-any.whl", hash = "sha256:752dc31160cdbd0436bb93bad51560b57e525cbb1d4bbf6f4904ceee75548241"},
+    {file = "fastapi-0.104.1.tar.gz", hash = "sha256:e5e4540a7c5e1dcfbbcf5b903c234feddcdcd881f191977a1c5dfd917487e7ae"},
 ]
 
 [package.dependencies]
-pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
+anyio = ">=3.7.1,<4.0.0"
+pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0 || >2.0.0,<2.0.1 || >2.0.1,<2.1.0 || >2.1.0,<3.0.0"
 starlette = ">=0.27.0,<0.28.0"
-typing-extensions = ">=4.5.0"
+typing-extensions = ">=4.8.0"
 
 [package.extras]
-all = ["email-validator (>=1.1.1)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "python-multipart (>=0.0.5)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"]
+all = ["email-validator (>=2.0.0)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)", "jinja2 (>=2.11.2)", "orjson (>=3.2.1)", "pydantic-extra-types (>=2.0.0)", "pydantic-settings (>=2.0.0)", "python-multipart (>=0.0.5)", "pyyaml (>=5.3.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0)", "uvicorn[standard] (>=0.12.0)"]
 
 [[package]]
 name = "fastjsonschema"
-version = "2.18.0"
+version = "2.19.0"
 description = "Fastest Python implementation of JSON schema"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "fastjsonschema-2.18.0-py3-none-any.whl", hash = "sha256:128039912a11a807068a7c87d0da36660afbfd7202780db26c4aa7153cfdc799"},
-    {file = "fastjsonschema-2.18.0.tar.gz", hash = "sha256:e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd"},
+    {file = "fastjsonschema-2.19.0-py3-none-any.whl", hash = "sha256:b9fd1a2dd6971dbc7fee280a95bd199ae0dd9ce22beb91cc75e9c1c528a5170e"},
+    {file = "fastjsonschema-2.19.0.tar.gz", hash = "sha256:e25df6647e1bc4a26070b700897b07b542ec898dd4f1f6ea013e7f6a88417225"},
 ]
 
 [package.extras]
@@ -1443,7 +1364,6 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 name = "fastobo"
 version = "0.12.2"
 description = "Faultless AST for Open Biomedical Ontologies in Python."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1488,25 +1408,24 @@ files = [
 
 [[package]]
 name = "filelock"
-version = "3.12.2"
+version = "3.13.1"
 description = "A platform independent file lock."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.12.2-py3-none-any.whl", hash = "sha256:cbb791cdea2a72f23da6ac5b5269ab0a0d161e9ef0100e653b69049a7706d1ec"},
-    {file = "filelock-3.12.2.tar.gz", hash = "sha256:002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81"},
+    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
+    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
 name = "flatbuffers"
 version = "23.5.26"
 description = "The FlatBuffers serialization format for Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1516,50 +1435,57 @@ files = [
 
 [[package]]
 name = "fonttools"
-version = "4.42.1"
+version = "4.46.0"
 description = "Tools to manipulate font files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "fonttools-4.46.0-cp39-cp39-win_amd64.whl", hash = "sha256:5200b01f463d97cc2b7ff8a1e3584151f4413e98cb8419da5f17d1dbb84cc214"},
+    {file = "fonttools-4.46.0-py3-none-any.whl", hash = "sha256:5b627ed142398ea9202bd752c04311592558964d1a765fb2f78dc441a05633f4"},
+    {file = "fonttools-4.46.0.tar.gz", hash = "sha256:2ae45716c27a41807d58a9f3f59983bdc8c0a46cb259e4450ab7e196253a9853"},
+]
+
+[package.extras]
+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
 interpolatable = ["munkres", "scipy"]
 lxml = ["lxml (>=4.0,<5)"]
@@ -1569,14 +1495,13 @@ repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
-unicode = ["unicodedata2 (>=15.0.0)"]
+unicode = ["unicodedata2 (>=15.1.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "fqdn"
 version = "1.5.1"
 description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
 files = [
@@ -1588,7 +1513,6 @@ files = [
 name = "free-proxy"
 version = "1.1.1"
 description = "Proxy scraper for further use"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1603,7 +1527,6 @@ requests = "*"
 name = "frozenlist"
 version = "1.4.0"
 description = "A list-like structure which implements collections.abc.MutableSequence"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1672,14 +1595,13 @@ files = [
 
 [[package]]
 name = "fsspec"
-version = "2023.6.0"
+version = "2023.12.0"
 description = "File-system specification"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "fsspec-2023.6.0-py3-none-any.whl", hash = "sha256:1cbad1faef3e391fba6dc005ae9b5bdcbf43005c9167ce78c915549c352c869a"},
-    {file = "fsspec-2023.6.0.tar.gz", hash = "sha256:d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af"},
+    {file = "fsspec-2023.12.0-py3-none-any.whl", hash = "sha256:f807252ee2018f2223760315beb87a2166c2b9532786eeca9e6548dfcf2cfac9"},
+    {file = "fsspec-2023.12.0.tar.gz", hash = "sha256:8e0bb2db2a94082968483b7ba2eaebf3949835e2dfdf09243dda387539464b31"},
 ]
 
 [package.extras]
@@ -1710,7 +1632,6 @@ tqdm = ["tqdm"]
 name = "funowl"
 version = "0.2.3"
 description = "Python rendering of the OWL Functional syntax"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1728,14 +1649,13 @@ rfc3987 = "*"
 
 [[package]]
 name = "furo"
-version = "2023.8.19"
+version = "2023.9.10"
 description = "A clean customisable Sphinx documentation theme."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "furo-2023.8.19-py3-none-any.whl", hash = "sha256:12f99f87a1873b6746228cfde18f77244e6c1ffb85d7fed95e638aae70d80590"},
-    {file = "furo-2023.8.19.tar.gz", hash = "sha256:e671ee638ab3f1b472f4033b0167f502ab407830e0db0f843b1c1028119c9cd1"},
+    {file = "furo-2023.9.10-py3-none-any.whl", hash = "sha256:513092538537dc5c596691da06e3c370714ec99bc438680edc1debffb73e5bfc"},
+    {file = "furo-2023.9.10.tar.gz", hash = "sha256:5707530a476d2a63b8cad83b4f961f3739a69f4b058bcf38a03a39fa537195b2"},
 ]
 
 [package.dependencies]
@@ -1748,7 +1668,6 @@ sphinx-basic-ng = "*"
 name = "ghp-import"
 version = "2.1.0"
 description = "Copy your docs directly to the gh-pages branch."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1764,14 +1683,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "gitdb"
-version = "4.0.10"
+version = "4.0.11"
 description = "Git Object Database"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "gitdb-4.0.10-py3-none-any.whl", hash = "sha256:c286cf298426064079ed96a9e4a9d39e7f3e9bf15ba60701e95f5492f28415c7"},
-    {file = "gitdb-4.0.10.tar.gz", hash = "sha256:6eb990b69df4e15bad899ea868dc46572c3f75339735663b81de79b06f17eb9a"},
+    {file = "gitdb-4.0.11-py3-none-any.whl", hash = "sha256:81a3407ddd2ee8df444cbacea00e2d038e40150acfa3001696fe0dcf1d3adfa4"},
+    {file = "gitdb-4.0.11.tar.gz", hash = "sha256:bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b"},
 ]
 
 [package.dependencies]
@@ -1779,29 +1697,30 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.32"
+version = "3.1.40"
 description = "GitPython is a Python library used to interact with Git repositories"
-category = "main"
 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-3.1.40-py3-none-any.whl", hash = "sha256:cf14627d5a8049ffbf49915732e5eddbe8134c3bdb9d476e6182b676fc573f8a"},
+    {file = "GitPython-3.1.40.tar.gz", hash = "sha256:22b126e9ffb671fdd0c129796343a02bf67bf2994b35449ffc9321aa755e18a4"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
+[package.extras]
+test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-instafail", "pytest-subtests", "pytest-sugar"]
+
 [[package]]
 name = "google-api-core"
-version = "2.11.1"
+version = "2.14.0"
 description = "Google API client core library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-core-2.11.1.tar.gz", hash = "sha256:25d29e05a0058ed5f19c61c0a78b1b53adea4d9364b464d014fbda941f6d1c9a"},
-    {file = "google_api_core-2.11.1-py3-none-any.whl", hash = "sha256:d92a5a92dc36dd4f4b9ee4e55528a90e432b059f93aee6ad857f9de8cc7ae94a"},
+    {file = "google-api-core-2.14.0.tar.gz", hash = "sha256:5368a4502b793d9bbf812a5912e13e4e69f9bd87f6efb508460c43f5bbd1ce41"},
+    {file = "google_api_core-2.14.0-py3-none-any.whl", hash = "sha256:de2fb50ed34d47ddbb2bd2dcf680ee8fead46279f4ed6b16de362aca23a18952"},
 ]
 
 [package.dependencies]
@@ -1817,18 +1736,17 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 
 [[package]]
 name = "google-api-python-client"
-version = "2.97.0"
+version = "2.109.0"
 description = "Google API Client Library for Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-api-python-client-2.97.0.tar.gz", hash = "sha256:48277291894876a1ca7ed4127e055e81f81e6343ced1b544a7200ae2c119dcd7"},
-    {file = "google_api_python_client-2.97.0-py2.py3-none-any.whl", hash = "sha256:5215f4cd577753fc4192ccfbe0bb8b55d4bb5fd68fa6268ac5cf271b6305de31"},
+    {file = "google-api-python-client-2.109.0.tar.gz", hash = "sha256:d06390c25477c361d52639fe00ef912c3fab8dafc7fbf29580c1144e92523a79"},
+    {file = "google_api_python_client-2.109.0-py2.py3-none-any.whl", hash = "sha256:72e7d46cc70908d808e29f16d983b441783fe56b694cec132db9af9fb991daa2"},
 ]
 
 [package.dependencies]
-google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0.dev0"
+google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0.dev0"
 google-auth = ">=1.19.0,<3.0.0.dev0"
 google-auth-httplib2 = ">=0.1.0"
 httplib2 = ">=0.15.0,<1.dev0"
@@ -1836,22 +1754,19 @@ uritemplate = ">=3.0.1,<5"
 
 [[package]]
 name = "google-auth"
-version = "2.22.0"
+version = "2.24.0"
 description = "Google Authentication Library"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "google-auth-2.22.0.tar.gz", hash = "sha256:164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce"},
-    {file = "google_auth-2.22.0-py2.py3-none-any.whl", hash = "sha256:d61d1b40897407b574da67da1a833bdc10d5a11642566e506565d1b1a46ba873"},
+    {file = "google-auth-2.24.0.tar.gz", hash = "sha256:2ec7b2a506989d7dbfdbe81cb8d0ead8876caaed14f86d29d34483cbe99c57af"},
+    {file = "google_auth-2.24.0-py2.py3-none-any.whl", hash = "sha256:9b82d5c8d3479a5391ea0a46d81cca698d328459da31d4a459d4e901a5d927e0"},
 ]
 
 [package.dependencies]
 cachetools = ">=2.0.0,<6.0"
 pyasn1-modules = ">=0.2.1"
 rsa = ">=3.1.4,<5"
-six = ">=1.9.0"
-urllib3 = "<2.0"
 
 [package.extras]
 aiohttp = ["aiohttp (>=3.6.2,<4.0.0.dev0)", "requests (>=2.20.0,<3.0.0.dev0)"]
@@ -1862,31 +1777,28 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
 
 [[package]]
 name = "google-auth-httplib2"
-version = "0.1.0"
+version = "0.1.1"
 description = "Google Authentication Library: httplib2 transport"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "google-auth-httplib2-0.1.0.tar.gz", hash = "sha256:a07c39fd632becacd3f07718dfd6021bf396978f03ad3ce4321d060015cc30ac"},
-    {file = "google_auth_httplib2-0.1.0-py2.py3-none-any.whl", hash = "sha256:31e49c36c6b5643b57e82617cb3e021e3e1d2df9da63af67252c02fa9c1f4a10"},
+    {file = "google-auth-httplib2-0.1.1.tar.gz", hash = "sha256:c64bc555fdc6dd788ea62ecf7bccffcf497bf77244887a3f3d7a5a02f8e3fc29"},
+    {file = "google_auth_httplib2-0.1.1-py2.py3-none-any.whl", hash = "sha256:42c50900b8e4dcdf8222364d1f0efe32b8421fb6ed72f2613f12f75cc933478c"},
 ]
 
 [package.dependencies]
 google-auth = "*"
-httplib2 = ">=0.15.0"
-six = "*"
+httplib2 = ">=0.19.0"
 
 [[package]]
 name = "google-auth-oauthlib"
-version = "1.0.0"
+version = "1.1.0"
 description = "Google Authentication Library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "google-auth-oauthlib-1.0.0.tar.gz", hash = "sha256:e375064964820b47221a7e1b7ee1fd77051b6323c3f9e3e19785f78ab67ecfc5"},
-    {file = "google_auth_oauthlib-1.0.0-py2.py3-none-any.whl", hash = "sha256:95880ca704928c300f48194d1770cf5b1462835b6e49db61445a520f793fd5fb"},
+    {file = "google-auth-oauthlib-1.1.0.tar.gz", hash = "sha256:83ea8c3b0881e453790baff4448e8a6112ac8778d1de9da0b68010b843937afb"},
+    {file = "google_auth_oauthlib-1.1.0-py2.py3-none-any.whl", hash = "sha256:089c6e587d36f4803ac7e0720c045c6a8b1fd1790088b8424975b90d0ee61c12"},
 ]
 
 [package.dependencies]
@@ -1900,7 +1812,6 @@ tool = ["click (>=6.0.0)"]
 name = "google-search-results"
 version = "2.4.2"
 description = "Scrape and search localized results from Google, Bing, Baidu, Yahoo, Yandex, Ebay, Homedepot, youtube at scale using SerpApi.com"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1912,14 +1823,13 @@ requests = "*"
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.60.0"
+version = "1.61.0"
 description = "Common protobufs used in Google APIs"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1930,15 +1840,14 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"]
 
 [[package]]
 name = "gpt4all"
-version = "1.0.8"
+version = "1.0.12"
 description = "Python bindings for GPT4All"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1952,7 +1861,6 @@ dev = ["black", "isort", "mkautodoc", "mkdocs-jupyter", "mkdocs-material", "mkdo
 name = "graphviz"
 version = "0.20.1"
 description = "Simple Python interface for Graphviz"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1969,7 +1877,6 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=
 name = "greenlet"
 version = "2.0.1"
 description = "Lightweight in-process concurrent programming"
-category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 files = [
@@ -2043,7 +1950,6 @@ test = ["faulthandler", "objgraph", "psutil"]
 name = "grpcio"
 version = "1.59.3"
 description = "HTTP/2-based RPC framework"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2108,14 +2014,13 @@ protobuf = ["grpcio-tools (>=1.59.3)"]
 
 [[package]]
 name = "gspread"
-version = "5.10.0"
+version = "5.12.1"
 description = "Google Spreadsheets Python API"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -2126,7 +2031,6 @@ google-auth-oauthlib = ">=0.4.1"
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 version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2138,7 +2042,6 @@ files = [
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 version = "0.9.1"
 description = "Honey Badger reader - a generic file/url/string open and read tool"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2150,7 +2053,6 @@ files = [
 name = "httpcore"
 version = "0.17.3"
 description = "A minimal low-level HTTP client."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2162,17 +2064,16 @@ files = [
 anyio = ">=3.0,<5.0"
 certifi = "*"
 h11 = ">=0.13,<0.15"
-sniffio = ">=1.0.0,<2.0.0"
+sniffio = "==1.*"
 
 [package.extras]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
+socks = ["socksio (==1.*)"]
 
 [[package]]
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 version = "0.22.0"
 description = "A comprehensive HTTP client library."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
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 [[package]]
 name = "httptools"
-version = "0.6.0"
+version = "0.6.1"
 description = "A collection of framework independent HTTP protocol utils."
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+    {file = "httptools-0.6.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:dcbab042cc3ef272adc11220517278519adf8f53fd3056d0e68f0a6f891ba94e"},
+    {file = "httptools-0.6.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:0cf2372e98406efb42e93bfe10f2948e467edfd792b015f1b4ecd897903d3e8d"},
+    {file = "httptools-0.6.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:678fcbae74477a17d103b7cae78b74800d795d702083867ce160fc202104d0da"},
+    {file = "httptools-0.6.1-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:e0b281cf5a125c35f7f6722b65d8542d2e57331be573e9e88bc8b0115c4a7a81"},
+    {file = "httptools-0.6.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:95658c342529bba4e1d3d2b1a874db16c7cca435e8827422154c9da76ac4e13a"},
+    {file = "httptools-0.6.1-cp39-cp39-win_amd64.whl", hash = "sha256:7ebaec1bf683e4bf5e9fbb49b8cc36da482033596a415b3e4ebab5a4c0d7ec5e"},
+    {file = "httptools-0.6.1.tar.gz", hash = "sha256:c6e26c30455600b95d94b1b836085138e82f177351454ee841c148f93a9bad5a"},
 ]
 
 [package.extras]
@@ -2235,7 +2136,6 @@ test = ["Cython (>=0.29.24,<0.30.0)"]
 name = "httpx"
 version = "0.24.1"
 description = "The next generation HTTP client."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2251,25 +2151,24 @@ sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
-cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<14)"]
+cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
+socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "huggingface-hub"
-version = "0.16.4"
+version = "0.19.4"
 description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub"
-category = "main"
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.8.0"
 files = [
-    {file = "huggingface_hub-0.16.4-py3-none-any.whl", hash = "sha256:0d3df29932f334fead024afc7cb4cc5149d955238b8b5e42dcf9740d6995a349"},
-    {file = "huggingface_hub-0.16.4.tar.gz", hash = "sha256:608c7d4f3d368b326d1747f91523dbd1f692871e8e2e7a4750314a2dd8b63e14"},
+    {file = "huggingface_hub-0.19.4-py3-none-any.whl", hash = "sha256:dba013f779da16f14b606492828f3760600a1e1801432d09fe1c33e50b825bb5"},
+    {file = "huggingface_hub-0.19.4.tar.gz", hash = "sha256:176a4fc355a851c17550e7619488f383189727eab209534d7cef2114dae77b22"},
 ]
 
 [package.dependencies]
 filelock = "*"
-fsspec = "*"
+fsspec = ">=2023.5.0"
 packaging = ">=20.9"
 pyyaml = ">=5.1"
 requests = "*"
@@ -2277,22 +2176,22 @@ tqdm = ">=4.42.1"
 typing-extensions = ">=3.7.4.3"
 
 [package.extras]
-all = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "black (>=23.1,<24.0)", "gradio", "jedi", "mypy (==0.982)", "numpy", "pydantic", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-vcr", "pytest-xdist", "ruff (>=0.0.241)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "urllib3 (<2.0)"]
+all = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jedi", "mypy (==1.5.1)", "numpy", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-vcr", "pytest-xdist", "ruff (>=0.1.3)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)"]
 cli = ["InquirerPy (==0.3.4)"]
-dev = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "black (>=23.1,<24.0)", "gradio", "jedi", "mypy (==0.982)", "numpy", "pydantic", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-vcr", "pytest-xdist", "ruff (>=0.0.241)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "urllib3 (<2.0)"]
+dev = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jedi", "mypy (==1.5.1)", "numpy", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-vcr", "pytest-xdist", "ruff (>=0.1.3)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)"]
+docs = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "hf-doc-builder", "jedi", "mypy (==1.5.1)", "numpy", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-vcr", "pytest-xdist", "ruff (>=0.1.3)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)", "watchdog"]
 fastai = ["fastai (>=2.4)", "fastcore (>=1.3.27)", "toml"]
-inference = ["aiohttp", "pydantic"]
-quality = ["black (>=23.1,<24.0)", "mypy (==0.982)", "ruff (>=0.0.241)"]
+inference = ["aiohttp", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)"]
+quality = ["mypy (==1.5.1)", "ruff (>=0.1.3)"]
 tensorflow = ["graphviz", "pydot", "tensorflow"]
-testing = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jedi", "numpy", "pydantic", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-vcr", "pytest-xdist", "soundfile", "urllib3 (<2.0)"]
+testing = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "gradio", "jedi", "numpy", "pydantic (>1.1,<2.0)", "pydantic (>1.1,<3.0)", "pytest", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-vcr", "pytest-xdist", "soundfile", "urllib3 (<2.0)"]
 torch = ["torch"]
-typing = ["pydantic", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3"]
+typing = ["types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)"]
 
 [[package]]
 name = "humanfriendly"
 version = "10.0"
 description = "Human friendly output for text interfaces using Python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -2305,21 +2204,19 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
-    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+    {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
+    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
 [[package]]
 name = "ijson"
 version = "3.2.3"
 description = "Iterative JSON parser with standard Python iterator interfaces"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2345,6 +2242,17 @@ files = [
     {file = "ijson-3.2.3-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:4a3a6a2fbbe7550ffe52d151cf76065e6b89cfb3e9d0463e49a7e322a25d0426"},
     {file = "ijson-3.2.3-cp311-cp311-win32.whl", hash = "sha256:6a4db2f7fb9acfb855c9ae1aae602e4648dd1f88804a0d5cfb78c3639bcf156c"},
     {file = "ijson-3.2.3-cp311-cp311-win_amd64.whl", hash = "sha256:ccd6be56335cbb845f3d3021b1766299c056c70c4c9165fb2fbe2d62258bae3f"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:055b71bbc37af5c3c5861afe789e15211d2d3d06ac51ee5a647adf4def19c0ea"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:c075a547de32f265a5dd139ab2035900fef6653951628862e5cdce0d101af557"},
+    {file = "ijson-3.2.3-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:457f8a5fc559478ac6b06b6d37ebacb4811f8c5156e997f0d87d708b0d8ab2ae"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:9788f0c915351f41f0e69ec2618b81ebfcf9f13d9d67c6d404c7f5afda3e4afb"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:fa234ab7a6a33ed51494d9d2197fb96296f9217ecae57f5551a55589091e7853"},
+    {file = "ijson-3.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bdd0dc5da4f9dc6d12ab6e8e0c57d8b41d3c8f9ceed31a99dae7b2baf9ea769a"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:c6beb80df19713e39e68dc5c337b5c76d36ccf69c30b79034634e5e4c14d6904"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:a2973ce57afb142d96f35a14e9cfec08308ef178a2c76b8b5e1e98f3960438bf"},
+    {file = "ijson-3.2.3-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:105c314fd624e81ed20f925271ec506523b8dd236589ab6c0208b8707d652a0e"},
+    {file = "ijson-3.2.3-cp312-cp312-win32.whl", hash = "sha256:ac44781de5e901ce8339352bb5594fcb3b94ced315a34dbe840b4cff3450e23b"},
+    {file = "ijson-3.2.3-cp312-cp312-win_amd64.whl", hash = "sha256:0567e8c833825b119e74e10a7c29761dc65fcd155f5d4cb10f9d3b8916ef9912"},
     {file = "ijson-3.2.3-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:eeb286639649fb6bed37997a5e30eefcacddac79476d24128348ec890b2a0ccb"},
     {file = "ijson-3.2.3-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:396338a655fb9af4ac59dd09c189885b51fa0eefc84d35408662031023c110d1"},
     {file = "ijson-3.2.3-cp36-cp36m-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:0e0243d166d11a2a47c17c7e885debf3b19ed136be2af1f5d1c34212850236ac"},
@@ -2407,7 +2315,6 @@ files = [
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -2417,48 +2324,45 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "7.0.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
-    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
+    {file = "importlib_metadata-7.0.0-py3-none-any.whl", hash = "sha256:d97503976bb81f40a193d41ee6570868479c69d5068651eb039c40d850c59d67"},
+    {file = "importlib_metadata-7.0.0.tar.gz", hash = "sha256:7fc841f8b8332803464e5dc1c63a2e59121f46ca186c0e2e182e80bf8c1319f7"},
 ]
 
 [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"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.0.1"
+version = "6.1.1"
 description = "Read resources from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.0.1-py3-none-any.whl", hash = "sha256:134832a506243891221b88b4ae1213327eea96ceb4e407a00d790bb0626f45cf"},
-    {file = "importlib_resources-6.0.1.tar.gz", hash = "sha256:4359457e42708462b9626a04657c6208ad799ceb41e5c58c57ffa0e6a098a5d4"},
+    {file = "importlib_resources-6.1.1-py3-none-any.whl", hash = "sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6"},
+    {file = "importlib_resources-6.1.1.tar.gz", hash = "sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
 
 [[package]]
 name = "inflection"
 version = "0.5.1"
 description = "A port of Ruby on Rails inflector to Python"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2470,7 +2374,6 @@ files = [
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2482,7 +2385,6 @@ files = [
 name = "intervaltree"
 version = "3.1.0"
 description = "Editable interval tree data structure for Python 2 and 3"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -2494,14 +2396,13 @@ sortedcontainers = ">=2.0,<3.0"
 
 [[package]]
 name = "ipykernel"
-version = "6.25.1"
+version = "6.27.1"
 description = "IPython Kernel for Jupyter"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.25.1-py3-none-any.whl", hash = "sha256:c8a2430b357073b37c76c21c52184db42f6b4b0e438e1eb7df3c4440d120497c"},
-    {file = "ipykernel-6.25.1.tar.gz", hash = "sha256:050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f"},
+    {file = "ipykernel-6.27.1-py3-none-any.whl", hash = "sha256:dab88b47f112f9f7df62236511023c9bdeef67abc73af7c652e4ce4441601686"},
+    {file = "ipykernel-6.27.1.tar.gz", hash = "sha256:7d5d594b6690654b4d299edba5e872dc17bb7396a8d0609c97cb7b8a1c605de6"},
 ]
 
 [package.dependencies]
@@ -2510,7 +2411,7 @@ comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
@@ -2528,74 +2429,58 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio"
 
 [[package]]
 name = "ipython"
-version = "8.14.0"
+version = "8.18.1"
 description = "IPython: Productive Interactive Computing"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "ipython-8.14.0-py3-none-any.whl", hash = "sha256:248aca623f5c99a6635bc3857677b7320b9b8039f99f070ee0d20a5ca5a8e6bf"},
-    {file = "ipython-8.14.0.tar.gz", hash = "sha256:1d197b907b6ba441b692c48cf2a3a2de280dc0ac91a3405b39349a50272ca0a1"},
+    {file = "ipython-8.18.1-py3-none-any.whl", hash = "sha256:e8267419d72d81955ec1177f8a29aaa90ac80ad647499201119e2f05e99aa397"},
+    {file = "ipython-8.18.1.tar.gz", hash = "sha256:ca6f079bb33457c66e233e4580ebfc4128855b4cf6370dddd73842a9563e8a27"},
 ]
 
 [package.dependencies]
-appnope = {version = "*", markers = "sys_platform == \"darwin\""}
-backcall = "*"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
+exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
-pickleshare = "*"
-prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
+prompt-toolkit = ">=3.0.41,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
 typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
-all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
+all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
-doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
 notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
-
-[[package]]
-name = "ipython-genutils"
-version = "0.2.0"
-description = "Vestigial utilities from IPython"
-category = "dev"
-optional = false
-python-versions = "*"
-files = [
-    {file = "ipython_genutils-0.2.0-py2.py3-none-any.whl", hash = "sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8"},
-    {file = "ipython_genutils-0.2.0.tar.gz", hash = "sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"},
-]
+test = ["pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath", "trio"]
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.0"
+version = "8.1.1"
 description = "Jupyter interactive widgets"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ipywidgets-8.1.0-py3-none-any.whl", hash = "sha256:6c8396cc7b8c95dfb4e9ab0054f48c002f045e7e5d7ae523f559d64e525a98ab"},
-    {file = "ipywidgets-8.1.0.tar.gz", hash = "sha256:ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687"},
+    {file = "ipywidgets-8.1.1-py3-none-any.whl", hash = "sha256:2b88d728656aea3bbfd05d32c747cfd0078f9d7e159cf982433b58ad717eed7f"},
+    {file = "ipywidgets-8.1.1.tar.gz", hash = "sha256:40211efb556adec6fa450ccc2a77d59ca44a060f4f9f136833df59c9f538e6e8"},
 ]
 
 [package.dependencies]
 comm = ">=0.1.3"
 ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0.7,<3.1.0"
+jupyterlab-widgets = ">=3.0.9,<3.1.0"
 traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.7,<4.1.0"
+widgetsnbextension = ">=4.0.9,<4.1.0"
 
 [package.extras]
 test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
@@ -2604,7 +2489,6 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
 name = "isodate"
 version = "0.6.1"
 description = "An ISO 8601 date/time/duration parser and formatter"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2619,7 +2503,6 @@ six = "*"
 name = "isoduration"
 version = "20.11.0"
 description = "Operations with ISO 8601 durations"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2632,14 +2515,13 @@ arrow = ">=0.15.0"
 
 [[package]]
 name = "jedi"
-version = "0.19.0"
+version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "jedi-0.19.0-py2.py3-none-any.whl", hash = "sha256:cb8ce23fbccff0025e9386b5cf85e892f94c9b822378f8da49970471335ac64e"},
-    {file = "jedi-0.19.0.tar.gz", hash = "sha256:bcf9894f1753969cbac8022a8c2eaee06bfa3724e4192470aaffe7eb6272b0c4"},
+    {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
+    {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
 ]
 
 [package.dependencies]
@@ -2648,13 +2530,12 @@ parso = ">=0.8.3,<0.9.0"
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
 [[package]]
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2672,7 +2553,6 @@ i18n = ["Babel (>=2.7)"]
 name = "joblib"
 version = "1.3.2"
 description = "Lightweight pipelining with Python functions"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2682,13 +2562,12 @@ files = [
 
 [[package]]
 name = "jsbeautifier"
-version = "1.14.9"
+version = "1.14.11"
 description = "JavaScript unobfuscator and beautifier."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "jsbeautifier-1.14.9.tar.gz", hash = "sha256:c738ebc36b47bd94e4ca6dd17a9004c3cc74edad582ca1d60e0e5d5945a63cb9"},
+    {file = "jsbeautifier-1.14.11.tar.gz", hash = "sha256:6b632581ea60dd1c133cd25a48ad187b4b91f526623c4b0fb5443ef805250505"},
 ]
 
 [package.dependencies]
@@ -2699,7 +2578,6 @@ six = ">=1.13.0"
 name = "json-flattener"
 version = "0.1.9"
 description = "Python library for denormalizing nested dicts or json objects to tables and back"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -2715,7 +2593,6 @@ pyyaml = "*"
 name = "json5"
 version = "0.9.14"
 description = "A Python implementation of the JSON5 data format."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2730,7 +2607,6 @@ dev = ["hypothesis"]
 name = "jsonasobj"
 version = "1.3.1"
 description = "JSON as python objects"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2742,7 +2618,6 @@ files = [
 name = "jsonasobj2"
 version = "1.0.4"
 description = "JSON as python objects - version 2"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2757,7 +2632,6 @@ hbreader = "*"
 name = "jsonlines"
 version = "3.1.0"
 description = "Library with helpers for the jsonlines file format"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2772,7 +2646,6 @@ attrs = ">=19.2.0"
 name = "jsonpatch"
 version = "1.33"
 description = "Apply JSON-Patches (RFC 6902)"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -2785,27 +2658,22 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpath-ng"
-version = "1.5.3"
+version = "1.6.0"
 description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "jsonpath-ng-1.5.3.tar.gz", hash = "sha256:a273b182a82c1256daab86a313b937059261b5c5f8c4fa3fc38b882b344dd567"},
-    {file = "jsonpath_ng-1.5.3-py2-none-any.whl", hash = "sha256:f75b95dbecb8a0f3b86fd2ead21c2b022c3f5770957492b9b6196ecccfeb10aa"},
-    {file = "jsonpath_ng-1.5.3-py3-none-any.whl", hash = "sha256:292a93569d74029ba75ac2dc3d3630fc0e17b2df26119a165fa1d498ca47bf65"},
+    {file = "jsonpath-ng-1.6.0.tar.gz", hash = "sha256:5483f8e9d74c39c9abfab554c070ae783c1c8cbadf5df60d561bc705ac68a07e"},
+    {file = "jsonpath_ng-1.6.0-py3-none-any.whl", hash = "sha256:6fd04833412c4b3d9299edf369542f5e67095ca84efa17cbb7f06a34958adc9f"},
 ]
 
 [package.dependencies]
-decorator = "*"
 ply = "*"
-six = "*"
 
 [[package]]
 name = "jsonpointer"
 version = "2.4"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -2815,30 +2683,29 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.0"
+version = "4.20.0"
 description = "An implementation of JSON Schema validation for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
-    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
+    {file = "jsonschema-4.20.0-py3-none-any.whl", hash = "sha256:ed6231f0429ecf966f5bc8dfef245998220549cbbcf140f913b7464c52c3b6b3"},
+    {file = "jsonschema-4.20.0.tar.gz", hash = "sha256:4f614fd46d8d61258610998997743ec5492a648b33cf478c1ddc23ed4598a5fa"},
 ]
 
 [package.dependencies]
 attrs = ">=22.2.0"
-fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
+fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
+idna = {version = "*", optional = true, markers = "extra == \"format\""}
+isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
 jsonschema-specifications = ">=2023.03.6"
 referencing = ">=0.28.4"
-rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
 rpds-py = ">=0.7.1"
-uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
+uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
+webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
@@ -2846,24 +2713,22 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.7.1"
+version = "2023.11.2"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
-    {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
+    {file = "jsonschema_specifications-2023.11.2-py3-none-any.whl", hash = "sha256:e74ba7c0a65e8cb49dc26837d6cfe576557084a8b423ed16a420984228104f93"},
+    {file = "jsonschema_specifications-2023.11.2.tar.gz", hash = "sha256:9472fc4fea474cd74bea4a2b190daeccb5a9e4db2ea80efcf7a1b582fc9a81b8"},
 ]
 
 [package.dependencies]
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter"
 version = "1.0.0"
 description = "Jupyter metapackage. Install all the Jupyter components in one go."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2882,19 +2747,18 @@ qtconsole = "*"
 
 [[package]]
 name = "jupyter-client"
-version = "8.3.0"
+version = "8.6.0"
 description = "Jupyter protocol implementation and client libraries"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-8.3.0-py3-none-any.whl", hash = "sha256:7441af0c0672edc5d28035e92ba5e32fadcfa8a4e608a434c228836a89df6158"},
-    {file = "jupyter_client-8.3.0.tar.gz", hash = "sha256:3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f"},
+    {file = "jupyter_client-8.6.0-py3-none-any.whl", hash = "sha256:909c474dbe62582ae62b758bca86d6518c85234bdee2d908c778db6d72f39d99"},
+    {file = "jupyter_client-8.6.0.tar.gz", hash = "sha256:0642244bb83b4764ae60d07e010e15f0e2d275ec4e918a8f7b80fbbef3ca60c7"},
 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
@@ -2908,7 +2772,6 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 name = "jupyter-console"
 version = "6.6.3"
 description = "Jupyter terminal console"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2920,7 +2783,7 @@ files = [
 ipykernel = ">=6.14"
 ipython = "*"
 jupyter-client = ">=7.0.0"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 prompt-toolkit = ">=3.0.30"
 pygments = "*"
 pyzmq = ">=17"
@@ -2931,14 +2794,13 @@ test = ["flaky", "pexpect", "pytest"]
 
 [[package]]
 name = "jupyter-core"
-version = "5.3.1"
+version = "5.5.0"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_core-5.3.1-py3-none-any.whl", hash = "sha256:ae9036db959a71ec1cac33081eeb040a79e681f08ab68b0883e9a676c7a90dce"},
-    {file = "jupyter_core-5.3.1.tar.gz", hash = "sha256:5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba"},
+    {file = "jupyter_core-5.5.0-py3-none-any.whl", hash = "sha256:e11e02cd8ae0a9de5c6c44abf5727df9f2581055afe00b22183f621ba3585805"},
+    {file = "jupyter_core-5.5.0.tar.gz", hash = "sha256:880b86053bf298a8724994f95e99b99130659022a4f7f45f563084b6223861d3"},
 ]
 
 [package.dependencies]
@@ -2947,19 +2809,18 @@ pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_
 traitlets = ">=5.3"
 
 [package.extras]
-docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
 test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-events"
-version = "0.7.0"
+version = "0.9.0"
 description = "Jupyter Event System library"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_events-0.7.0-py3-none-any.whl", hash = "sha256:4753da434c13a37c3f3c89b500afa0c0a6241633441421f6adafe2fb2e2b924e"},
-    {file = "jupyter_events-0.7.0.tar.gz", hash = "sha256:7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615"},
+    {file = "jupyter_events-0.9.0-py3-none-any.whl", hash = "sha256:d853b3c10273ff9bc8bb8b30076d65e2c9685579db736873de6c2232dde148bf"},
+    {file = "jupyter_events-0.9.0.tar.gz", hash = "sha256:81ad2e4bc710881ec274d31c6c50669d71bbaa5dd9d01e600b56faa85700d399"},
 ]
 
 [package.dependencies]
@@ -2978,14 +2839,13 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
 
 [[package]]
 name = "jupyter-lsp"
-version = "2.2.0"
+version = "2.2.1"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter-lsp-2.2.0.tar.gz", hash = "sha256:8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1"},
-    {file = "jupyter_lsp-2.2.0-py3-none-any.whl", hash = "sha256:9e06b8b4f7dd50300b70dd1a78c0c3b0c3d8fa68e0f2d8a5d1fbab62072aca3f"},
+    {file = "jupyter-lsp-2.2.1.tar.gz", hash = "sha256:b17fab6d70fe83c8896b0cff59237640038247c196056b43684a0902b6a9e0fb"},
+    {file = "jupyter_lsp-2.2.1-py3-none-any.whl", hash = "sha256:17a689910c5e4ae5e7d334b02f31d08ffbe98108f6f658fb05e4304b4345368b"},
 ]
 
 [package.dependencies]
@@ -2994,14 +2854,13 @@ jupyter-server = ">=1.1.2"
 
 [[package]]
 name = "jupyter-server"
-version = "2.7.2"
+version = "2.11.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_server-2.7.2-py3-none-any.whl", hash = "sha256:98a375347b580e837e7016007c24680a4261ed8ad7cd35196ac087d229f48e5a"},
-    {file = "jupyter_server-2.7.2.tar.gz", hash = "sha256:d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523"},
+    {file = "jupyter_server-2.11.2-py3-none-any.whl", hash = "sha256:0c548151b54bcb516ca466ec628f7f021545be137d01b5467877e87f6fff4374"},
+    {file = "jupyter_server-2.11.2.tar.gz", hash = "sha256:0c99f9367b0f24141e527544522430176613f9249849be80504c6d2b955004bb"},
 ]
 
 [package.dependencies]
@@ -3009,8 +2868,8 @@ anyio = ">=3.1.0"
 argon2-cffi = "*"
 jinja2 = "*"
 jupyter-client = ">=7.4.4"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
-jupyter-events = ">=0.6.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-events = ">=0.9.0"
 jupyter-server-terminals = "*"
 nbconvert = ">=6.4.4"
 nbformat = ">=5.3.0"
@@ -3033,7 +2892,6 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc
 name = "jupyter-server-terminals"
 version = "0.4.4"
 description = "A Jupyter Server Extension Providing Terminals."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3051,14 +2909,13 @@ test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov",
 
 [[package]]
 name = "jupyterlab"
-version = "4.0.5"
+version = "4.0.9"
 description = "JupyterLab computational environment"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab-4.0.5-py3-none-any.whl", hash = "sha256:13b3a326e7b95d72746fe20dbe80ee1e71165d6905e01ceaf1320eb809cb1b47"},
-    {file = "jupyterlab-4.0.5.tar.gz", hash = "sha256:de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611"},
+    {file = "jupyterlab-4.0.9-py3-none-any.whl", hash = "sha256:9f6f8e36d543fdbcc3df961a1d6a3f524b4a4001be0327a398f68fa4e534107c"},
+    {file = "jupyterlab-4.0.9.tar.gz", hash = "sha256:9ebada41d52651f623c0c9f069ddb8a21d6848e4c887d8e5ddc0613166ed5c0b"},
 ]
 
 [package.dependencies]
@@ -3077,33 +2934,31 @@ tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["black[jupyter] (==23.3.0)", "build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.0.271)"]
-docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-tornasync", "sphinx (>=1.8)", "sphinx-copybutton"]
+dev = ["black[jupyter] (==23.10.1)", "build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.1.4)"]
+docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-tornasync", "sphinx (>=1.8,<7.2.0)", "sphinx-copybutton"]
 docs-screenshots = ["altair (==5.0.1)", "ipython (==8.14.0)", "ipywidgets (==8.0.6)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.0.post0)", "matplotlib (==3.7.1)", "nbconvert (>=7.0.0)", "pandas (==2.0.2)", "scipy (==1.10.1)", "vega-datasets (==0.9.0)"]
 test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter (>=0.5.3)", "pytest-timeout", "pytest-tornasync", "requests", "requests-cache", "virtualenv"]
 
 [[package]]
 name = "jupyterlab-pygments"
-version = "0.2.2"
+version = "0.3.0"
 description = "Pygments theme using JupyterLab CSS variables"
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab_pygments-0.2.2-py2.py3-none-any.whl", hash = "sha256:2405800db07c9f770863bcf8049a529c3dd4d3e28536638bd7c1c01d2748309f"},
-    {file = "jupyterlab_pygments-0.2.2.tar.gz", hash = "sha256:7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d"},
+    {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"},
+    {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"},
 ]
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.24.0"
+version = "2.25.2"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "jupyterlab_server-2.24.0-py3-none-any.whl", hash = "sha256:5f077e142bb8dc9b843d960f940c513581bceca3793a0d80f9c67d9522c4e876"},
-    {file = "jupyterlab_server-2.24.0.tar.gz", hash = "sha256:4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07"},
+    {file = "jupyterlab_server-2.25.2-py3-none-any.whl", hash = "sha256:5b1798c9cc6a44f65c757de9f97fc06fc3d42535afbf47d2ace5e964ab447aaf"},
+    {file = "jupyterlab_server-2.25.2.tar.gz", hash = "sha256:bd0ec7a99ebcedc8bcff939ef86e52c378e44c2707e053fcd81d046ce979ee63"},
 ]
 
 [package.dependencies]
@@ -3111,33 +2966,31 @@ babel = ">=2.10"
 importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
 jinja2 = ">=3.0.3"
 json5 = ">=0.9.0"
-jsonschema = ">=4.17.3"
+jsonschema = ">=4.18.0"
 jupyter-server = ">=1.21,<3"
 packaging = ">=21.3"
-requests = ">=2.28"
+requests = ">=2.31"
 
 [package.extras]
 docs = ["autodoc-traits", "jinja2 (<3.2.0)", "mistune (<4)", "myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinxcontrib-openapi (>0.8)"]
-openapi = ["openapi-core (>=0.16.1,<0.17.0)", "ruamel-yaml"]
-test = ["hatch", "ipykernel", "jupyterlab-server[openapi]", "openapi-spec-validator (>=0.5.1,<0.7.0)", "pytest (>=7.0)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter[server] (>=0.6.2)", "pytest-timeout", "requests-mock", "sphinxcontrib-spelling", "strict-rfc3339", "werkzeug"]
+openapi = ["openapi-core (>=0.18.0,<0.19.0)", "ruamel-yaml"]
+test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-validator (>=0.6.0,<0.8.0)", "pytest (>=7.0)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter[server] (>=0.6.2)", "pytest-timeout", "requests-mock", "ruamel-yaml", "sphinxcontrib-spelling", "strict-rfc3339", "werkzeug"]
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.8"
+version = "3.0.9"
 description = "Jupyter interactive widgets for JupyterLab"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jupyterlab_widgets-3.0.8-py3-none-any.whl", hash = "sha256:4715912d6ceab839c9db35953c764b3214ebbc9161c809f6e0510168845dfdf5"},
-    {file = "jupyterlab_widgets-3.0.8.tar.gz", hash = "sha256:d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a"},
+    {file = "jupyterlab_widgets-3.0.9-py3-none-any.whl", hash = "sha256:3cf5bdf5b897bf3bccf1c11873aa4afd776d7430200f765e0686bd352487b58d"},
+    {file = "jupyterlab_widgets-3.0.9.tar.gz", hash = "sha256:6005a4e974c7beee84060fdfba341a3218495046de8ae3ec64888e5fe19fdb4c"},
 ]
 
 [[package]]
 name = "kgcl-rdflib"
 version = "0.5.0"
 description = "Schema for the KGCL project."
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -3153,7 +3006,6 @@ linkml-runtime = ">=1.1.24"
 name = "kgcl-schema"
 version = "0.6.0"
 description = "Schema for the KGCL project."
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -3171,7 +3023,6 @@ prefixmaps = ">=0.1.5,<0.2.0"
 name = "kiwisolver"
 version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3285,7 +3136,6 @@ files = [
 name = "kubernetes"
 version = "28.1.0"
 description = "Kubernetes python client"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3303,21 +3153,20 @@ requests = "*"
 requests-oauthlib = "*"
 six = ">=1.9.0"
 urllib3 = ">=1.24.2,<2.0"
-websocket-client = ">=0.32.0,<0.40.0 || >0.40.0,<0.41.0 || >=0.43.0"
+websocket-client = ">=0.32.0,<0.40.0 || >0.40.0,<0.41.dev0 || >=0.43.dev0"
 
 [package.extras]
 adal = ["adal (>=1.0.2)"]
 
 [[package]]
 name = "lark"
-version = "1.1.7"
+version = "1.1.8"
 description = "a modern parsing library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "lark-1.1.7-py3-none-any.whl", hash = "sha256:9e5dc5bbf93fa1840083707285262514a0ef8a6613874af7ea1cec60468d6e92"},
-    {file = "lark-1.1.7.tar.gz", hash = "sha256:be7437bf1f37ab08b355f29ff2571d77d777113d0a8c4352b0c513dced6c5a1e"},
+    {file = "lark-1.1.8-py3-none-any.whl", hash = "sha256:7d2c221a66a8165f3f81aacb958d26033d40d972fdb70213ab0a2e0627e29c86"},
+    {file = "lark-1.1.8.tar.gz", hash = "sha256:7ef424db57f59c1ffd6f0d4c2b705119927f566b68c0fe1942dddcc0e44391a5"},
 ]
 
 [package.extras]
@@ -3328,14 +3177,13 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.5.7"
+version = "1.6.3"
 description = "Linked Open Data Modeling Language"
-category = "dev"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
+python-versions = ">=3.8.1,<4.0.0"
 files = [
-    {file = "linkml-1.5.7-py3-none-any.whl", hash = "sha256:677f4c5809dc51b151b86accc69e77482ad86b9c1326a212cef9b4a2a9a96c10"},
-    {file = "linkml-1.5.7.tar.gz", hash = "sha256:bca3dd56837ced79749656843e1e20b8d1db1a89287e7b29d1ee145e4a75ad4d"},
+    {file = "linkml-1.6.3-py3-none-any.whl", hash = "sha256:2bcfa9e35b3e0d868f396fa48ede1b9e3c6016df956dd5ca92d70ff621ffc77e"},
+    {file = "linkml-1.6.3.tar.gz", hash = "sha256:2692243c9fb1c262ea83b725c70d6f537844ae7a9405101c94bccf65def6d952"},
 ]
 
 [package.dependencies]
@@ -3348,12 +3196,12 @@ jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
 linkml-dataops = "*"
-linkml-runtime = ">=1.5.4"
+linkml-runtime = ">=1.6.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
 prefixmaps = ">=0.1.3"
-pydantic = "*"
+pydantic = ">=1.0.0,<3.0.0"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
 pyshexc = ">=0.8.3"
@@ -3368,7 +3216,6 @@ watchdog = ">=0.9.0"
 name = "linkml-dataops"
 version = "0.1.0"
 description = "LinkML Data Operations API"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3387,7 +3234,6 @@ linkml-runtime = ">=1.1.6"
 name = "linkml-renderer"
 version = "0.3.0"
 description = "linkml-renderer"
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -3403,14 +3249,13 @@ pydantic = "*"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.6.0"
+version = "1.6.2"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
-category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml_runtime-1.6.0-py3-none-any.whl", hash = "sha256:1b6b698f8cf23d63ff833ae0be8055b2e945e1c0ef06a1ed6db359247194a2eb"},
-    {file = "linkml_runtime-1.6.0.tar.gz", hash = "sha256:a06df7431a9b929afe242598800d99cec83bb31cbdc1f5d2d70e6b26c67dc337"},
+    {file = "linkml_runtime-1.6.2-py3-none-any.whl", hash = "sha256:d9a915faf0ee8c8749f42d38394a06d37f016e155e077ff9cb5c5a21f24e19d6"},
+    {file = "linkml_runtime-1.6.2.tar.gz", hash = "sha256:bcbeff96d24433276755db85375e3dff0c9af0fd04f8a05f7ccd8a669a9e9877"},
 ]
 
 [package.dependencies]
@@ -3432,7 +3277,6 @@ requests = "*"
 name = "llm"
 version = "0.12"
 description = "A CLI utility and Python library for interacting with Large Language Models, including OpenAI, PaLM and local models installed on your own machine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3460,7 +3304,6 @@ test = ["black", "cogapp", "mypy", "numpy", "pytest", "requests-mock", "ruff", "
 name = "llm-gpt4all"
 version = "0.1.1"
 description = "Plugin for LLM adding support for GPT4ALL models"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3480,7 +3323,6 @@ test = ["pytest"]
 name = "lxml"
 version = "4.9.3"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
 files = [
@@ -3586,28 +3428,26 @@ source = ["Cython (>=0.29.35)"]
 
 [[package]]
 name = "markdown"
-version = "3.4.4"
+version = "3.5.1"
 description = "Python implementation of John Gruber's Markdown."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Markdown-3.4.4-py3-none-any.whl", hash = "sha256:a4c1b65c0957b4bd9e7d86ddc7b3c9868fb9670660f6f99f6d1bca8954d5a941"},
-    {file = "Markdown-3.4.4.tar.gz", hash = "sha256:225c6123522495d4119a90b3a3ba31a1e87a70369e03f14799ea9c0d7183a3d6"},
+    {file = "Markdown-3.5.1-py3-none-any.whl", hash = "sha256:5874b47d4ee3f0b14d764324d2c94c03ea66bee56f2d929da9f2508d65e722dc"},
+    {file = "Markdown-3.5.1.tar.gz", hash = "sha256:b65d7beb248dc22f2e8a31fb706d93798093c308dc1aba295aedeb9d41a813bd"},
 ]
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.0)", "mkdocs-nature (>=0.4)"]
+docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.5)", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-nature (>=0.6)", "mkdocs-section-index", "mkdocstrings[python]"]
 testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markdown-it-py"
 version = "3.0.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3628,28 +3468,10 @@ profiling = ["gprof2dot"]
 rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
-[[package]]
-name = "markdown2"
-version = "2.4.10"
-description = "A fast and complete Python implementation of Markdown"
-category = "main"
-optional = false
-python-versions = ">=3.5, <4"
-files = [
-    {file = "markdown2-2.4.10-py2.py3-none-any.whl", hash = "sha256:e6105800483783831f5dc54f827aa5b44eb137ecef5a70293d8ecfbb4109ecc6"},
-    {file = "markdown2-2.4.10.tar.gz", hash = "sha256:cdba126d90dc3aef6f4070ac342f974d63f415678959329cc7909f96cc235d72"},
-]
-
-[package.extras]
-all = ["pygments (>=2.7.3)", "wavedrom"]
-code-syntax-highlighting = ["pygments (>=2.7.3)"]
-wavedrom = ["wavedrom"]
-
 [[package]]
 name = "markupsafe"
 version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3717,53 +3539,39 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.7.2"
+version = "3.8.2"
 description = "Python plotting package"
-category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "matplotlib-3.7.2-cp310-cp310-macosx_10_12_universal2.whl", hash = "sha256:2699f7e73a76d4c110f4f25be9d2496d6ab4f17345307738557d345f099e07de"},
-    {file = "matplotlib-3.7.2-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:a8035ba590658bae7562786c9cc6ea1a84aa49d3afab157e414c9e2ea74f496d"},
-    {file = "matplotlib-3.7.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2f8e4a49493add46ad4a8c92f63e19d548b2b6ebbed75c6b4c7f46f57d36cdd1"},
-    {file = "matplotlib-3.7.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:71667eb2ccca4c3537d9414b1bc00554cb7f91527c17ee4ec38027201f8f1603"},
-    {file = "matplotlib-3.7.2-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:152ee0b569a37630d8628534c628456b28686e085d51394da6b71ef84c4da201"},
-    {file = "matplotlib-3.7.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:070f8dddd1f5939e60aacb8fa08f19551f4b0140fab16a3669d5cd6e9cb28fc8"},
-    {file = "matplotlib-3.7.2-cp310-cp310-win32.whl", hash = "sha256:fdbb46fad4fb47443b5b8ac76904b2e7a66556844f33370861b4788db0f8816a"},
-    {file = "matplotlib-3.7.2-cp310-cp310-win_amd64.whl", hash = "sha256:23fb1750934e5f0128f9423db27c474aa32534cec21f7b2153262b066a581fd1"},
-    {file = "matplotlib-3.7.2-cp311-cp311-macosx_10_12_universal2.whl", hash = "sha256:30e1409b857aa8a747c5d4f85f63a79e479835f8dffc52992ac1f3f25837b544"},
-    {file = "matplotlib-3.7.2-cp311-cp311-macosx_10_12_x86_64.whl", hash = "sha256:50e0a55ec74bf2d7a0ebf50ac580a209582c2dd0f7ab51bc270f1b4a0027454e"},
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 ]
 
 [package.dependencies]
@@ -3771,18 +3579,17 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
-numpy = ">=1.20"
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+numpy = ">=1.21,<2"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
-pyparsing = ">=2.3.1,<3.1"
+pillow = ">=8"
+pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
 [[package]]
 name = "matplotlib-inline"
 version = "0.1.6"
 description = "Inline Matplotlib backend for Jupyter"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3797,7 +3604,6 @@ traitlets = "*"
 name = "mdit-py-plugins"
 version = "0.4.0"
 description = "Collection of plugins for markdown-it-py"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3817,7 +3623,6 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "mdurl"
 version = "0.1.2"
 description = "Markdown URL utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3829,7 +3634,6 @@ files = [
 name = "mergedeep"
 version = "1.3.4"
 description = "A deep merge function for 🐍."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3839,26 +3643,24 @@ files = [
 
 [[package]]
 name = "mistune"
-version = "3.0.1"
+version = "3.0.2"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "mkdocs"
-version = "1.5.2"
+version = "1.5.3"
 description = "Project documentation with Markdown."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -3883,48 +3685,48 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 
 [[package]]
 name = "mkdocs-material"
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+version = "9.4.14"
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-pymdown-extensions = ">=9.9.1"
-readtime = ">=2.0"
-regex = ">=2022.4.24"
-requests = ">=2.26"
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+colorama = ">=0.4,<1.0"
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+markdown = ">=3.2,<4.0"
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+pygments = ">=2.16,<3.0"
+pymdown-extensions = ">=10.2,<11.0"
+regex = ">=2022.4"
+requests = ">=2.26,<3.0"
+
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 [[package]]
 name = "mkdocs-material-extensions"
-version = "1.1.1"
+version = "1.3.1"
 description = "Extension pack for Python Markdown and MkDocs Material."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [[package]]
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 version = "0.6.0"
 description = "A MkDocs plugin for including mermaid graphs in markdown sources"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3946,7 +3748,6 @@ setuptools = ">=18.5"
 name = "monotonic"
 version = "1.6"
 description = "An implementation of time.monotonic() for Python 2 & < 3.3"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3958,7 +3759,6 @@ files = [
 name = "more-click"
 version = "0.1.2"
 description = "More click."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3976,7 +3776,6 @@ tests = ["coverage", "pytest"]
 name = "mpmath"
 version = "1.3.0"
 description = "Python library for arbitrary-precision floating-point arithmetic"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3994,7 +3793,6 @@ tests = ["pytest (>=4.6)"]
 name = "multidict"
 version = "6.0.4"
 description = "multidict implementation"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4078,7 +3876,6 @@ files = [
 name = "myst-parser"
 version = "2.0.0"
 description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4103,19 +3900,18 @@ testing-docutils = ["pygments", "pytest (>=7,<8)", "pytest-param-files (>=0.3.4,
 
 [[package]]
 name = "nbclient"
-version = "0.8.0"
+version = "0.9.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 ]
 
 [package.dependencies]
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 nbformat = ">=5.1"
 traitlets = ">=5.4"
 
@@ -4126,14 +3922,13 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
 [[package]]
 name = "nbconvert"
-version = "7.7.4"
+version = "7.12.0"
 description = "Converting Jupyter Notebooks"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "nbconvert-7.12.0.tar.gz", hash = "sha256:b1564bd89f69a74cd6398b0362da94db07aafb991b7857216a766204a71612c0"},
 ]
 
 [package.dependencies]
@@ -4160,14 +3955,13 @@ docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sp
 qtpdf = ["nbconvert[qtpng]"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
-test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pre-commit", "pytest", "pytest-dependency"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest"]
 webpdf = ["playwright"]
 
 [[package]]
 name = "nbformat"
 version = "5.9.2"
 description = "The Jupyter Notebook format"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4187,14 +3981,13 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "ndex2"
-version = "3.5.1"
+version = "3.6.0"
 description = "Nice CX Python includes a client and a data model."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -4209,40 +4002,37 @@ urllib3 = ">=1.16"
 
 [[package]]
 name = "nest-asyncio"
-version = "1.5.7"
+version = "1.5.8"
 description = "Patch asyncio to allow nested event loops"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
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 ]
 
 [[package]]
 name = "networkx"
-version = "3.1"
+version = "3.2.1"
 description = "Python package for creating and manipulating graphs and networks"
-category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
+default = ["matplotlib (>=3.5)", "numpy (>=1.22)", "pandas (>=1.4)", "scipy (>=1.9,!=1.11.0,!=1.11.1)"]
+developer = ["changelist (==0.4)", "mypy (>=1.1)", "pre-commit (>=3.2)", "rtoml"]
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+extra = ["lxml (>=4.6)", "pydot (>=1.4.2)", "pygraphviz (>=1.11)", "sympy (>=1.10)"]
+test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "nltk"
 version = "3.8.1"
 description = "Natural Language Toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4266,14 +4056,13 @@ twitter = ["twython"]
 
 [[package]]
 name = "notebook"
-version = "7.0.2"
+version = "7.0.6"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -4286,13 +4075,12 @@ tornado = ">=6.2.0"
 [package.extras]
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 docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
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+test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.22.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
 
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 version = "0.2.3"
 description = "A shim layer for notebook traits and config"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4308,49 +4096,199 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 
 [[package]]
 name = "numpy"
-version = "1.25.2"
+version = "1.26.2"
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 python-versions = ">=3.9"
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 [package.dependencies]
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 appdirs = ">=1.4.4"
 class-resolver = ">=0.4.2"
 click = "*"
-curies = ">=0.5.5"
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@@ -4386,12 +4324,12 @@ sssom-schema = ">=0.11.0"
 
 [package.extras]
 gilda = ["gilda (>=1.0.0)", "urllib3 (<2)"]
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 optional = false
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 version = "0.1.4"
 description = "A client to the EBI Ontology Lookup Service"
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 files = [
@@ -4429,36 +4366,35 @@ tests = ["coverage", "pytest"]
 
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 ]
 
 [package.dependencies]
@@ -4473,7 +4409,6 @@ sympy = "*"
 name = "ontoportal-client"
 version = "0.0.4"
 description = "A client to BioPortal and other OntoPortal instances."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4491,14 +4426,13 @@ tests = ["coverage", "pytest", "unittest-templates"]
 
 [[package]]
 name = "openai"
-version = "0.27.9"
+version = "0.28.1"
 description = "Python client library for the OpenAI API"
-category = "main"
 optional = false
 python-versions = ">=3.7.1"
 files = [
-    {file = "openai-0.27.9-py3-none-any.whl", hash = "sha256:6a3cf8e276d1a6262b50562fbc0cba7967cfebb78ed827d375986b48fdad6475"},
-    {file = "openai-0.27.9.tar.gz", hash = "sha256:b687761c82f5ebb6f61efc791b2083d2d068277b94802d4d1369efe39851813d"},
+    {file = "openai-0.28.1-py3-none-any.whl", hash = "sha256:d18690f9e3d31eedb66b57b88c2165d760b24ea0a01f150dd3f068155088ce68"},
+    {file = "openai-0.28.1.tar.gz", hash = "sha256:4be1dad329a65b4ce1a660fe6d5431b438f429b5855c883435f0f7fcb6d2dcc8"},
 ]
 
 [package.dependencies]
@@ -4508,7 +4442,7 @@ tqdm = "*"
 
 [package.extras]
 datalib = ["numpy", "openpyxl (>=3.0.7)", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)"]
-dev = ["black (>=21.6b0,<22.0)", "pytest (>=6.0.0,<7.0.0)", "pytest-asyncio", "pytest-mock"]
+dev = ["black (>=21.6b0,<22.0)", "pytest (==6.*)", "pytest-asyncio", "pytest-mock"]
 embeddings = ["matplotlib", "numpy", "openpyxl (>=3.0.7)", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)", "plotly", "scikit-learn (>=1.0.2)", "scipy", "tenacity (>=8.0.1)"]
 wandb = ["numpy", "openpyxl (>=3.0.7)", "pandas (>=1.2.3)", "pandas-stubs (>=1.1.0.11)", "wandb"]
 
@@ -4516,7 +4450,6 @@ wandb = ["numpy", "openpyxl (>=3.0.7)", "pandas (>=1.2.3)", "pandas-stubs (>=1.1
 name = "openpyxl"
 version = "3.1.2"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4529,71 +4462,50 @@ et-xmlfile = "*"
 
 [[package]]
 name = "opentelemetry-api"
-version = "1.21.0"
+version = "1.16.0"
 description = "OpenTelemetry Python API"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "opentelemetry_api-1.21.0-py3-none-any.whl", hash = "sha256:4bb86b28627b7e41098f0e93280fe4892a1abed1b79a19aec6f928f39b17dffb"},
-    {file = "opentelemetry_api-1.21.0.tar.gz", hash = "sha256:d6185fd5043e000075d921822fd2d26b953eba8ca21b1e2fa360dd46a7686316"},
+    {file = "opentelemetry_api-1.16.0-py3-none-any.whl", hash = "sha256:79e8f0cf88dbdd36b6abf175d2092af1efcaa2e71552d0d2b3b181a9707bf4bc"},
+    {file = "opentelemetry_api-1.16.0.tar.gz", hash = "sha256:4b0e895a3b1f5e1908043ebe492d33e33f9ccdbe6d02d3994c2f8721a63ddddb"},
 ]
 
 [package.dependencies]
 deprecated = ">=1.2.6"
-importlib-metadata = ">=6.0,<7.0"
-
-[[package]]
-name = "opentelemetry-exporter-otlp-proto-common"
-version = "1.21.0"
-description = "OpenTelemetry Protobuf encoding"
-category = "main"
-optional = false
-python-versions = ">=3.7"
-files = [
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-]
-
-[package.dependencies]
-backoff = {version = ">=1.10.0,<3.0.0", markers = "python_version >= \"3.7\""}
-opentelemetry-proto = "1.21.0"
+setuptools = ">=16.0"
 
 [[package]]
 name = "opentelemetry-exporter-otlp-proto-grpc"
-version = "1.21.0"
+version = "1.16.0"
 description = "OpenTelemetry Collector Protobuf over gRPC Exporter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 backoff = {version = ">=1.10.0,<3.0.0", markers = "python_version >= \"3.7\""}
-deprecated = ">=1.2.6"
 googleapis-common-protos = ">=1.52,<2.0"
 grpcio = ">=1.0.0,<2.0.0"
 opentelemetry-api = ">=1.15,<2.0"
-opentelemetry-exporter-otlp-proto-common = "1.21.0"
-opentelemetry-proto = "1.21.0"
-opentelemetry-sdk = ">=1.21.0,<1.22.0"
+opentelemetry-proto = "1.16.0"
+opentelemetry-sdk = ">=1.16.0,<1.17.0"
 
 [package.extras]
 test = ["pytest-grpc"]
 
 [[package]]
 name = "opentelemetry-proto"
-version = "1.21.0"
+version = "1.16.0"
 description = "OpenTelemetry Python Proto"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "opentelemetry_proto-1.16.0-py3-none-any.whl", hash = "sha256:160326d300faf43c3f72c4a916516ee5b63289ceb9828294b698ef943697cbd5"},
+    {file = "opentelemetry_proto-1.16.0.tar.gz", hash = "sha256:e58832dfec64621972a9836f8ae163fb3063946eb02bdf43fae0f76f8cf46d0a"},
 ]
 
 [package.dependencies]
@@ -4601,43 +4513,41 @@ protobuf = ">=3.19,<5.0"
 
 [[package]]
 name = "opentelemetry-sdk"
-version = "1.21.0"
+version = "1.16.0"
 description = "OpenTelemetry Python SDK"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "opentelemetry_sdk-1.16.0-py3-none-any.whl", hash = "sha256:15f03915eec4839f885a5e6ed959cde59b8690c8c012d07c95b4b138c98dc43f"},
+    {file = "opentelemetry_sdk-1.16.0.tar.gz", hash = "sha256:4d3bb91e9e209dbeea773b5565d901da4f76a29bf9dbc1c9500be3cabb239a4e"},
 ]
 
 [package.dependencies]
-opentelemetry-api = "1.21.0"
-opentelemetry-semantic-conventions = "0.42b0"
+opentelemetry-api = "1.16.0"
+opentelemetry-semantic-conventions = "0.37b0"
+setuptools = ">=16.0"
 typing-extensions = ">=3.7.4"
 
 [[package]]
 name = "opentelemetry-semantic-conventions"
-version = "0.42b0"
+version = "0.37b0"
 description = "OpenTelemetry Semantic Conventions"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "outcome"
-version = "1.2.0"
+version = "1.3.0.post0"
 description = "Capture the outcome of Python function calls."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -4647,7 +4557,6 @@ attrs = ">=19.2.0"
 name = "overrides"
 version = "7.4.0"
 description = "A decorator to automatically detect mismatch when overriding a method."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4657,21 +4566,19 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "23.1"
+version = "23.2"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "paginate"
 version = "0.5.6"
 description = "Divides large result sets into pages for easier browsing"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4680,77 +4587,76 @@ files = [
 
 [[package]]
 name = "pandas"
-version = "2.0.3"
+version = "2.1.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
-category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 numpy = [
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-    {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
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 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
 tzdata = ">=2022.1"
 
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 plot = ["matplotlib (>=3.6.1)"]
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 version = "1.5.0"
 description = "Utilities for writing pandoc filters in python"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -4762,7 +4668,6 @@ files = [
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 version = "0.0.1"
 description = "sqldf for pandas"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4777,21 +4682,19 @@ sqlalchemy = "*"
 
 [[package]]
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-version = "1.19.1"
+version = "1.20.0"
 description = "parse() is the opposite of format()"
-category = "dev"
 optional = false
 python-versions = "*"
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 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4807,7 +4710,6 @@ testing = ["docopt", "pytest (<6.0.0)"]
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 version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4817,105 +4719,79 @@ files = [
 
 [[package]]
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 description = "Pexpect allows easy control of interactive console applications."
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 python-versions = "*"
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 [package.dependencies]
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 ]
 
 [package.extras]
@@ -4924,26 +4800,24 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 
 [[package]]
 name = "pip"
-version = "23.2.1"
+version = "23.3.1"
 description = "The PyPA recommended tool for installing Python packages."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
 name = "platformdirs"
-version = "3.10.0"
+version = "4.1.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -4952,14 +4826,13 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -4970,7 +4843,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "ply"
 version = "3.11"
 description = "Python Lex & Yacc"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4980,14 +4852,13 @@ files = [
 
 [[package]]
 name = "posthog"
-version = "3.0.2"
+version = "3.1.0"
 description = "Integrate PostHog into any python application."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -5000,13 +4871,12 @@ six = ">=1.5"
 [package.extras]
 dev = ["black", "flake8", "flake8-print", "isort", "pre-commit"]
 sentry = ["django", "sentry-sdk"]
-test = ["coverage", "flake8", "freezegun (==0.3.15)", "mock (>=2.0.0)", "pylint", "pytest"]
+test = ["coverage", "flake8", "freezegun (==0.3.15)", "mock (>=2.0.0)", "pylint", "pytest", "pytest-timeout"]
 
 [[package]]
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 version = "0.1.12"
 description = "A python API for working with ID prefixes"
-category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -5024,7 +4894,6 @@ requests = ">=2.28.1,<3.0.0"
 name = "prefixmaps"
 version = "0.1.5"
 description = "A python library for retrieving semantic prefix maps"
-category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
@@ -5045,14 +4914,13 @@ refresh = ["bioregistry[refresh] (>=0.8.0,<0.9.0)", "rdflib[refresh] (>=6.2.0,<7
 
 [[package]]
 name = "prometheus-client"
-version = "0.17.1"
+version = "0.19.0"
 description = "Python client for the Prometheus monitoring system."
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -5060,14 +4928,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.39"
+version = "3.0.41"
 description = "Library for building powerful interactive command lines in Python"
-category = "dev"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -5077,7 +4944,6 @@ wcwidth = "*"
 name = "pronto"
 version = "2.5.5"
 description = "Python frontend to ontologies."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -5093,49 +4959,58 @@ python-dateutil = ">=2.8,<3.0"
 
 [[package]]
 name = "protobuf"
-version = "4.24.2"
-description = ""
-category = "main"
+version = "3.20.3"
+description = "Protocol Buffers"
 optional = false
 python-versions = ">=3.7"
 files = [
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 optional = false
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 [package.extras]
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 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
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 optional = false
 python-versions = "*"
 files = [
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 python-versions = "*"
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 [package.dependencies]
@@ -5205,7 +5078,6 @@ functions = ["apache-bookkeeper-client (>=4.16.1)", "grpcio (>=1.8.2)", "prometh
 name = "pure-eval"
 version = "0.2.2"
 description = "Safely evaluate AST nodes without side effects"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -5218,41 +5090,47 @@ tests = ["pytest"]
 
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 optional = false
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 version = "2.21"
 description = "C parser in Python"
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 version = "0.8.0"
 description = "Widget for deck.gl maps"
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 python-versions = ">=3.7"
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@@ -5390,24 +5346,23 @@ requests = ">=2.14.0"
 
 [[package]]
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 [package.extras]
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+    {file = "pymongo-4.6.1-cp39-cp39-manylinux2014_x86_64.whl", hash = "sha256:8ec75f35f62571a43e31e7bd11749d974c1b5cd5ea4a8388725d579263c0fdf6"},
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+    {file = "pymongo-4.6.1-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:9aafd036f6f2e5ad109aec92f8dbfcbe76cff16bad683eb6dd18013739c0b3ae"},
+    {file = "pymongo-4.6.1-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:1f2b856518bfcfa316c8dae3d7b412aecacf2e8ba30b149f5eb3b63128d703b9"},
+    {file = "pymongo-4.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5ec31adc2e988fd7db3ab509954791bbc5a452a03c85e45b804b4bfc31fa221d"},
+    {file = "pymongo-4.6.1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:9167e735379ec43d8eafa3fd675bfbb12e2c0464f98960586e9447d2cf2c7a83"},
+    {file = "pymongo-4.6.1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:1461199b07903fc1424709efafe379205bf5f738144b1a50a08b0396357b5abf"},
+    {file = "pymongo-4.6.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:3094c7d2f820eecabadae76bfec02669567bbdd1730eabce10a5764778564f7b"},
+    {file = "pymongo-4.6.1-cp39-cp39-win32.whl", hash = "sha256:c91ea3915425bd4111cb1b74511cdc56d1d16a683a48bf2a5a96b6a6c0f297f7"},
+    {file = "pymongo-4.6.1-cp39-cp39-win_amd64.whl", hash = "sha256:ef102a67ede70e1721fe27f75073b5314911dbb9bc27cde0a1c402a11531e7bd"},
+    {file = "pymongo-4.6.1.tar.gz", hash = "sha256:31dab1f3e1d0cdd57e8df01b645f52d43cc1b653ed3afd535d2891f4fc4f9712"},
 ]
 
 [package.dependencies]
@@ -5556,13 +5511,13 @@ encryption = ["certifi", "pymongo[aws]", "pymongocrypt (>=1.6.0,<2.0.0)"]
 gssapi = ["pykerberos", "winkerberos (>=0.5.0)"]
 ocsp = ["certifi", "cryptography (>=2.5)", "pyopenssl (>=17.2.0)", "requests (<3.0.0)", "service-identity (>=18.1.0)"]
 snappy = ["python-snappy"]
+test = ["pytest (>=7)"]
 zstd = ["zstandard"]
 
 [[package]]
 name = "pympler"
 version = "1.0.1"
 description = "A development tool to measure, monitor and analyze the memory behavior of Python objects."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -5574,7 +5529,6 @@ files = [
 name = "pynacl"
 version = "1.5.0"
 description = "Python binding to the Networking and Cryptography (NaCl) library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -5599,14 +5553,13 @@ tests = ["hypothesis (>=3.27.0)", "pytest (>=3.2.1,!=3.3.0)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.0.9"
+version = "3.1.1"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.6.8"
 files = [
-    {file = "pyparsing-3.0.9-py3-none-any.whl", hash = "sha256:5026bae9a10eeaefb61dab2f09052b9f4307d44aee4eda64b309723d8d206bbc"},
-    {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"},
+    {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
+    {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
 ]
 
 [package.extras]
@@ -5616,7 +5569,6 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pypika"
 version = "0.48.9"
 description = "A SQL query builder API for Python"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5625,14 +5577,13 @@ files = [
 
 [[package]]
 name = "pyproject-api"
-version = "1.5.4"
+version = "1.6.1"
 description = "API to interact with the python pyproject.toml based projects"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pyproject_api-1.5.4-py3-none-any.whl", hash = "sha256:ca462d457880340ceada078678a296ac500061cef77a040e1143004470ab0046"},
-    {file = "pyproject_api-1.5.4.tar.gz", hash = "sha256:8d41f3f0c04f0f6a830c27b1c425fa66699715ae06d8a054a1c5eeaaf8bfb145"},
+    {file = "pyproject_api-1.6.1-py3-none-any.whl", hash = "sha256:4c0116d60476b0786c88692cf4e325a9814965e2469c5998b830bba16b183675"},
+    {file = "pyproject_api-1.6.1.tar.gz", hash = "sha256:1817dc018adc0d1ff9ca1ed8c60e1623d5aaca40814b953af14a9cf9a5cae538"},
 ]
 
 [package.dependencies]
@@ -5640,33 +5591,13 @@ packaging = ">=23.1"
 tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "sphinx (<7.2)", "sphinx-autodoc-typehints (>=1.24)"]
-testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "setuptools (>=68)", "wheel (>=0.41.1)"]
-
-[[package]]
-name = "pyquery"
-version = "2.0.0"
-description = "A jquery-like library for python"
-category = "main"
-optional = false
-python-versions = "*"
-files = [
-    {file = "pyquery-2.0.0-py3-none-any.whl", hash = "sha256:8dfc9b4b7c5f877d619bbae74b1898d5743f6ca248cfd5d72b504dd614da312f"},
-    {file = "pyquery-2.0.0.tar.gz", hash = "sha256:963e8d4e90262ff6d8dec072ea97285dc374a2f69cad7776f4082abcf6a1d8ae"},
-]
-
-[package.dependencies]
-cssselect = ">=1.2.0"
-lxml = ">=2.1"
-
-[package.extras]
-test = ["pytest", "pytest-cov", "requests", "webob", "webtest"]
+docs = ["furo (>=2023.8.19)", "sphinx (<7.2)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "setuptools (>=68.1.2)", "wheel (>=0.41.2)"]
 
 [[package]]
 name = "pyreadline3"
 version = "3.4.1"
 description = "A python implementation of GNU readline."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5678,7 +5609,6 @@ files = [
 name = "pyshex"
 version = "0.8.1"
 description = "Python ShEx Implementation"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -5701,7 +5631,6 @@ urllib3 = "*"
 name = "pyshexc"
 version = "0.9.1"
 description = "PyShExC - Python ShEx compiler"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -5721,7 +5650,6 @@ shexjsg = ">=0.8.1"
 name = "pysocks"
 version = "1.7.1"
 description = "A Python SOCKS client module. See https://github.com/Anorov/PySocks for more information."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -5734,7 +5662,6 @@ files = [
 name = "pysolr"
 version = "3.9.0"
 description = "Lightweight Python client for Apache Solr"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5749,14 +5676,13 @@ solrcloud = ["kazoo (>=2.5.0)"]
 
 [[package]]
 name = "pystow"
-version = "0.5.0"
+version = "0.5.2"
 description = "Easily pick a place to store data for your python package."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pystow-0.5.0-py3-none-any.whl", hash = "sha256:816a9da33cd8a3f8fbda577c3d2957cfc99d1fa3ea45032dbfa087b9a21b630f"},
-    {file = "pystow-0.5.0.tar.gz", hash = "sha256:490e9ecbe4f947c72f63297f43f6584323c9ca2f2d48d47f2a22a815dc552bb4"},
+    {file = "pystow-0.5.2-py3-none-any.whl", hash = "sha256:c0faeb0fc854ede714be7949555f4d55ce40d8fd57f0ae1ff75e86158792299a"},
+    {file = "pystow-0.5.2.tar.gz", hash = "sha256:d05d233299d61b50f53c7de220d990ec4c58e3a54d195d8449f0302563eb6de6"},
 ]
 
 [package.dependencies]
@@ -5774,14 +5700,13 @@ xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "7.4.3"
 description = "pytest: simple powerful testing with Python"
-category = "main"
 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-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
+    {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
 ]
 
 [package.dependencies]
@@ -5799,7 +5724,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 name = "pytest-logging"
 version = "2015.11.4"
 description = "Configures logging and allows tweaking the log level with a py.test flag"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5813,7 +5737,6 @@ pytest = ">=2.8.1"
 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 = [
@@ -5828,7 +5751,6 @@ six = ">=1.5"
 name = "python-dotenv"
 version = "1.0.0"
 description = "Read key-value pairs from a .env file and set them as environment variables"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -5843,7 +5765,6 @@ cli = ["click (>=5.0)"]
 name = "python-json-logger"
 version = "2.0.7"
 description = "A python library adding a json log formatter"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -5853,13 +5774,13 @@ files = [
 
 [[package]]
 name = "python-pptx"
-version = "0.6.21"
+version = "0.6.23"
 description = "Generate and manipulate Open XML PowerPoint (.pptx) files"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
-    {file = "python-pptx-0.6.21.tar.gz", hash = "sha256:7798a2aaf89563565b3c7120c0acfe9aff775db0db3580544e3bf4840c2e378f"},
+    {file = "python-pptx-0.6.23.tar.gz", hash = "sha256:587497ff28e779ab18dbb074f6d4052893c85dedc95ed75df319364f331fedee"},
+    {file = "python_pptx-0.6.23-py3-none-any.whl", hash = "sha256:dd0527194627a2b7cc05f3ba23ecaa2d9a0d5ac9b6193a28ed1b7a716f4217d4"},
 ]
 
 [package.dependencies]
@@ -5871,7 +5792,6 @@ XlsxWriter = ">=0.5.7"
 name = "python-ulid"
 version = "1.1.0"
 description = "Universally Unique Lexicographically Sortable Identifier"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -5883,7 +5803,6 @@ files = [
 name = "pytrials"
 version = "0.3.0"
 description = "Python wrapper around the clinicaltrials.gov API"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -5898,7 +5817,6 @@ requests = "*"
 name = "pytrie"
 version = "0.4.0"
 description = "A pure Python implementation of the trie data structure."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5910,36 +5828,19 @@ sortedcontainers = "*"
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
-category = "main"
 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"},
-]
-
-[[package]]
-name = "pytz-deprecation-shim"
-version = "0.1.0.post0"
-description = "Shims to make deprecation of pytz easier"
-category = "main"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
-files = [
-    {file = "pytz_deprecation_shim-0.1.0.post0-py2.py3-none-any.whl", hash = "sha256:8314c9692a636c8eb3bda879b9f119e350e93223ae83e70e80c31675a0fdc1a6"},
-    {file = "pytz_deprecation_shim-0.1.0.post0.tar.gz", hash = "sha256:af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d"},
+    {file = "pytz-2023.3.post1-py2.py3-none-any.whl", hash = "sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"},
+    {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"},
 ]
 
-[package.dependencies]
-tzdata = {version = "*", markers = "python_version >= \"3.6\""}
-
 [[package]]
 name = "pywin32"
 version = "306"
 description = "Python for Window Extensions"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -5961,24 +5862,23 @@ files = [
 
 [[package]]
 name = "pywinpty"
-version = "2.0.11"
+version = "2.0.12"
 description = "Pseudo terminal support for Windows from Python."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pywinpty-2.0.11-cp310-none-win_amd64.whl", hash = "sha256:452f10ac9ff8ab9151aa8cea9e491a9612a12250b1899278c6a56bc184afb47f"},
-    {file = "pywinpty-2.0.11-cp311-none-win_amd64.whl", hash = "sha256:6701867d42aec1239bc0fedf49a336570eb60eb886e81763db77ea2b6c533cc3"},
-    {file = "pywinpty-2.0.11-cp38-none-win_amd64.whl", hash = "sha256:0ffd287751ad871141dc9724de70ea21f7fc2ff1af50861e0d232cf70739d8c4"},
-    {file = "pywinpty-2.0.11-cp39-none-win_amd64.whl", hash = "sha256:e4e7f023c28ca7aa8e1313e53ba80a4d10171fe27857b7e02f99882dfe3e8638"},
-    {file = "pywinpty-2.0.11.tar.gz", hash = "sha256:e244cffe29a894876e2cd251306efd0d8d64abd5ada0a46150a4a71c0b9ad5c5"},
+    {file = "pywinpty-2.0.12-cp310-none-win_amd64.whl", hash = "sha256:21319cd1d7c8844fb2c970fb3a55a3db5543f112ff9cfcd623746b9c47501575"},
+    {file = "pywinpty-2.0.12-cp311-none-win_amd64.whl", hash = "sha256:853985a8f48f4731a716653170cd735da36ffbdc79dcb4c7b7140bce11d8c722"},
+    {file = "pywinpty-2.0.12-cp312-none-win_amd64.whl", hash = "sha256:1617b729999eb6713590e17665052b1a6ae0ad76ee31e60b444147c5b6a35dca"},
+    {file = "pywinpty-2.0.12-cp38-none-win_amd64.whl", hash = "sha256:189380469ca143d06e19e19ff3fba0fcefe8b4a8cc942140a6b863aed7eebb2d"},
+    {file = "pywinpty-2.0.12-cp39-none-win_amd64.whl", hash = "sha256:7520575b6546db23e693cbd865db2764097bd6d4ef5dc18c92555904cd62c3d4"},
+    {file = "pywinpty-2.0.12.tar.gz", hash = "sha256:8197de460ae8ebb7f5d1701dfa1b5df45b157bb832e92acba316305e18ca00dd"},
 ]
 
 [[package]]
 name = "pyyaml"
 version = "6.0.1"
 description = "YAML parser and emitter for Python"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -6038,7 +5938,6 @@ files = [
 name = "pyyaml-env-tag"
 version = "0.1"
 description = "A custom YAML tag for referencing environment variables in YAML files. "
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -6053,7 +5952,6 @@ pyyaml = "*"
 name = "pyzmq"
 version = "25.1.1"
 description = "Python bindings for 0MQ"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -6157,25 +6055,23 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 
 [[package]]
 name = "qtconsole"
-version = "5.4.3"
+version = "5.5.1"
 description = "Jupyter Qt console"
-category = "dev"
 optional = false
-python-versions = ">= 3.7"
+python-versions = ">= 3.8"
 files = [
-    {file = "qtconsole-5.4.3-py3-none-any.whl", hash = "sha256:35fd6e87b1f6d1fd41801b07e69339f8982e76afd4fa8ef35595bc6036717189"},
-    {file = "qtconsole-5.4.3.tar.gz", hash = "sha256:5e4082a86a201796b2a5cfd4298352d22b158b51b57736531824715fc2a979dd"},
+    {file = "qtconsole-5.5.1-py3-none-any.whl", hash = "sha256:8c75fa3e9b4ed884880ff7cea90a1b67451219279ec33deaee1d59e3df1a5d2b"},
+    {file = "qtconsole-5.5.1.tar.gz", hash = "sha256:a0e806c6951db9490628e4df80caec9669b65149c7ba40f9bf033c025a5b56bc"},
 ]
 
 [package.dependencies]
 ipykernel = ">=4.1"
-ipython-genutils = "*"
 jupyter-client = ">=4.1"
 jupyter-core = "*"
 packaging = "*"
 pygments = "*"
 pyzmq = ">=17.1"
-qtpy = ">=2.0.1"
+qtpy = ">=2.4.0"
 traitlets = "<5.2.1 || >5.2.1,<5.2.2 || >5.2.2"
 
 [package.extras]
@@ -6184,14 +6080,13 @@ test = ["flaky", "pytest", "pytest-qt"]
 
 [[package]]
 name = "qtpy"
-version = "2.3.1"
+version = "2.4.1"
 description = "Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6)."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "QtPy-2.3.1-py3-none-any.whl", hash = "sha256:5193d20e0b16e4d9d3bc2c642d04d9f4e2c892590bd1b9c92bfe38a95d5a2e12"},
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 [package.dependencies]
@@ -6204,7 +6099,6 @@ test = ["pytest (>=6,!=7.0.0,!=7.0.1)", "pytest-cov (>=3.0.0)", "pytest-qt"]
 name = "ratelimit"
 version = "2.2.1"
 description = "API rate limit decorator"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -6215,7 +6109,6 @@ files = [
 name = "ratelimiter"
 version = "1.2.0.post0"
 description = "Simple python rate limiting object"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -6230,7 +6123,6 @@ test = ["pytest (>=3.0)", "pytest-asyncio"]
 name = "rdflib"
 version = "7.0.0"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
-category = "main"
 optional = false
 python-versions = ">=3.8.1,<4.0.0"
 files = [
@@ -6252,7 +6144,6 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"]
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 version = "0.6.1"
 description = "rdflib extension adding JSON-LD parser and serializer"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -6267,7 +6158,6 @@ rdflib = ">=5.0.0"
 name = "rdflib-shim"
 version = "1.0.3"
 description = "Shim for rdflib 5 and 6 incompatibilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6279,32 +6169,15 @@ files = [
 rdflib = ">=5.0.0"
 rdflib-jsonld = "0.6.1"
 
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-version = "3.0.0"
-description = "Calculates the time some text takes the average human to read, based on Medium's read time forumula"
-category = "main"
-optional = false
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-markdown2 = ">=2.4.3"
-pyquery = ">=1.2"
-
 [[package]]
 name = "referencing"
-version = "0.30.2"
+version = "0.31.1"
 description = "JSON Referencing + Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
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@@ -6313,107 +6186,105 @@ rpds-py = ">=0.7.0"
 
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+version = "2023.10.3"
 description = "Alternative regular expression module, to replace re."
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 version = "2.31.0"
 description = "Python HTTP for Humans."
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 python-versions = ">=3.7"
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@@ -6434,14 +6305,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "requests-cache"
-version = "1.1.0"
+version = "1.1.1"
 description = "A persistent cache for python requests"
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 version = "1.3.1"
 description = "OAuthlib authentication support for Requests."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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@@ -6486,7 +6355,6 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"]
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 description = "A utility belt for advanced users of python-requests"
-category = "main"
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@@ -6501,7 +6369,6 @@ requests = ">=2.0.1,<3.0.0"
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-category = "dev"
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@@ -6516,7 +6383,6 @@ six = "*"
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-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -6538,14 +6403,13 @@ files = [
 
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 python-versions = ">=3.6,<4"
 files = [
@@ -6679,155 +6543,204 @@ pyasn1 = ">=0.1.3"
 
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 [package.dependencies]
 joblib = ">=1.1.1"
-numpy = ">=1.17.3"
+numpy = ">=1.17.3,<2.0"
 scipy = ">=1.5.0"
 threadpoolctl = ">=2.0.0"
 
@@ -6897,48 +6814,50 @@ tests = ["black (>=23.3.0)", "matplotlib (>=3.1.3)", "mypy (>=1.3)", "numpydoc (
 
 [[package]]
 name = "scipy"
-version = "1.9.3"
+version = "1.11.4"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-
-[package.extras]
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-test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
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+]
+
+[package.dependencies]
+numpy = ">=1.21.6,<1.28.0"
+
+[package.extras]
+dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
+doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
+test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "seaborn"
 version = "0.12.2"
 description = "Statistical data visualization"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -6958,14 +6877,13 @@ stats = ["scipy (>=1.3)", "statsmodels (>=0.10)"]
 
 [[package]]
 name = "selenium"
-version = "4.11.2"
+version = "4.15.2"
 description = ""
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "selenium-4.11.2-py3-none-any.whl", hash = "sha256:98e72117b194b3fa9c69b48998f44bf7dd4152c7bd98544911a1753b9f03cc7d"},
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+    {file = "selenium-4.15.2.tar.gz", hash = "sha256:22eab5a1724c73d51b240a69ca702997b717eee4ba1f6065bf5d6b44dba01d48"},
 ]
 
 [package.dependencies]
@@ -6978,7 +6896,6 @@ urllib3 = {version = ">=1.26,<3", extras = ["socks"]}
 name = "semsimian"
 version = "0.2.1"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7023,7 +6940,6 @@ files = [
 name = "semsql"
 version = "0.3.2"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -7040,7 +6956,6 @@ SQLAlchemy-Utils = ">=0.38.2,<0.39.0"
 name = "send2trash"
 version = "1.8.2"
 description = "Send file to trash natively under Mac OS X, Windows and Linux"
-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
 files = [
@@ -7057,7 +6972,6 @@ win32 = ["pywin32"]
 name = "sentence-transformers"
 version = "2.2.2"
 description = "Multilingual text embeddings"
-category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -7080,7 +6994,6 @@ transformers = ">=4.6.0,<5.0.0"
 name = "sentencepiece"
 version = "0.1.99"
 description = "SentencePiece python wrapper"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -7133,26 +7046,24 @@ files = [
 
 [[package]]
 name = "setuptools"
-version = "68.1.2"
+version = "69.0.2"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-68.1.2-py3-none-any.whl", hash = "sha256:3d8083eed2d13afc9426f227b24fd1659489ec107c0e86cec2ffdde5c92e790b"},
-    {file = "setuptools-68.1.2.tar.gz", hash = "sha256:3d4dfa6d95f1b101d695a6160a7626e15583af71a5f52176efa5d39a054d475d"},
+    {file = "setuptools-69.0.2-py3-none-any.whl", hash = "sha256:1e8fdff6797d3865f37397be788a4e3cba233608e9b509382a2777d25ebde7f2"},
+    {file = "setuptools-69.0.2.tar.gz", hash = "sha256:735896e78a4742605974de002ac60562d286fa8051a7e2299445e8e8fbb01aa6"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5,<=7.1.2)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
 testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "shexjsg"
 version = "0.8.2"
 description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -7167,7 +7078,6 @@ pyjsg = ">=0.11.10"
 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 = [
@@ -7177,21 +7087,19 @@ files = [
 
 [[package]]
 name = "smmap"
-version = "5.0.0"
+version = "5.0.1"
 description = "A pure Python implementation of a sliding window memory map manager"
-category = "main"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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+    {file = "smmap-5.0.1-py3-none-any.whl", hash = "sha256:e6d8668fa5f93e706934a62d7b4db19c8d9eb8cf2adbb75ef1b675aa332b69da"},
+    {file = "smmap-5.0.1.tar.gz", hash = "sha256:dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62"},
 ]
 
 [[package]]
 name = "sniffio"
 version = "1.3.0"
 description = "Sniff out which async library your code is running under"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7203,7 +7111,6 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -7215,7 +7122,6 @@ files = [
 name = "sortedcontainers"
 version = "2.4.0"
 description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -7225,21 +7131,19 @@ files = [
 
 [[package]]
 name = "soupsieve"
-version = "2.4.1"
+version = "2.5"
 description = "A modern CSS selector implementation for Beautiful Soup."
-category = "main"
 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]]
 name = "sparqlslurper"
 version = "0.5.1"
 description = "SPARQL Slurper for rdflib"
-category = "dev"
 optional = false
 python-versions = ">=3.7.4"
 files = [
@@ -7256,7 +7160,6 @@ sparqlwrapper = ">=1.8.2"
 name = "sparqlwrapper"
 version = "2.0.0"
 description = "SPARQL Endpoint interface to Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7277,7 +7180,6 @@ pandas = ["pandas (>=1.3.5)"]
 name = "speechrecognition"
 version = "3.10.0"
 description = "Library for performing speech recognition, with support for several engines and APIs, online and offline."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -7293,14 +7195,13 @@ whisper-api = ["openai"]
 
 [[package]]
 name = "sphinx"
-version = "7.2.3"
+version = "7.2.6"
 description = "Python documentation generator"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "sphinx-7.2.6-py3-none-any.whl", hash = "sha256:1e09160a40b956dc623c910118fa636da93bd3ca0b9876a7b3df90f07d691560"},
+    {file = "sphinx-7.2.6.tar.gz", hash = "sha256:9a5160e1ea90688d5963ba09a2dcd8bdd526620edbb65c328728f1b2228d5ab5"},
 ]
 
 [package.dependencies]
@@ -7330,30 +7231,28 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools
 
 [[package]]
 name = "sphinx-autodoc-typehints"
-version = "1.24.0"
+version = "1.25.2"
 description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "sphinx_autodoc_typehints-1.25.2-py3-none-any.whl", hash = "sha256:5ed05017d23ad4b937eab3bee9fae9ab0dd63f0b42aa360031f1fad47e47f673"},
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 ]
 
 [package.dependencies]
-furo = {version = ">=2023.5.20", optional = true, markers = "extra == \"docs\""}
-sphinx = ">=7.0.1"
+furo = {version = ">=2023.7.26", optional = true, markers = "extra == \"docs\""}
+sphinx = ">=7.1.2"
 
 [package.extras]
-docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)"]
+docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)"]
 numpy = ["nptyping (>=2.5)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "sphobjinv (>=2.3.1)", "typing-extensions (>=4.6.3)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "sphobjinv (>=2.3.1)", "typing-extensions (>=4.7.1)"]
 
 [[package]]
 name = "sphinx-automodapi"
 version = "0.16.0"
 description = "Sphinx extension for auto-generating API documentation for entire modules"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7372,7 +7271,6 @@ test = ["coverage", "cython", "pytest", "pytest-cov", "setuptools"]
 name = "sphinx-basic-ng"
 version = "1.0.0b2"
 description = "A modern skeleton for Sphinx themes."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7388,14 +7286,13 @@ docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-ta
 
 [[package]]
 name = "sphinx-click"
-version = "5.0.1"
+version = "5.1.0"
 description = "Sphinx extension that automatically documents click applications"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -7405,19 +7302,18 @@ sphinx = ">=2.0"
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "1.3.0"
+version = "2.0.0"
 description = "Read the Docs theme for Sphinx"
-category = "main"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.6"
 files = [
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+    {file = "sphinx_rtd_theme-2.0.0-py2.py3-none-any.whl", hash = "sha256:ec93d0856dc280cf3aee9a4c9807c60e027c7f7b461b77aeffed682e68f0e586"},
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 [package.dependencies]
-docutils = "<0.19"
-sphinx = ">=1.6,<8"
+docutils = "<0.21"
+sphinx = ">=5,<8"
 sphinxcontrib-jquery = ">=4,<5"
 
 [package.extras]
@@ -7427,7 +7323,6 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 name = "sphinxcontrib-applehelp"
 version = "1.0.7"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -7446,7 +7341,6 @@ test = ["pytest"]
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 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -7465,7 +7359,6 @@ test = ["pytest"]
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 version = "2.0.4"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -7484,7 +7377,6 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jquery"
 version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
-category = "main"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -7499,7 +7391,6 @@ Sphinx = ">=1.8"
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -7514,7 +7405,6 @@ test = ["flake8", "mypy", "pytest"]
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 version = "1.0.6"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
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 python-versions = ">=3.9"
 files = [
@@ -7533,7 +7423,6 @@ test = ["pytest"]
 name = "sphinxcontrib-serializinghtml"
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 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -7552,7 +7441,6 @@ test = ["pytest"]
 name = "sphinxcontrib-websupport"
 version = "1.2.6"
 description = "sphinxcontrib-websupport provides a Python API to easily integrate Sphinx documentation into your Web application"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -7571,53 +7459,60 @@ test = ["greenlet (>=3.0.0a1)", "pytest", "sqlalchemy", "whoosh"]
 
 [[package]]
 name = "sqlalchemy"
-version = "2.0.20"
+version = "2.0.23"
 description = "Database Abstraction Library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
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+    {file = "SQLAlchemy-2.0.23.tar.gz", hash = "sha256:c1bda93cbbe4aa2aa0aa8655c5aeda505cd219ff3e8da91d1d329e143e4aff69"},
 ]
 
 [package.dependencies]
@@ -7626,6 +7521,7 @@ typing-extensions = ">=4.2.0"
 
 [package.extras]
 aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
+aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
@@ -7636,7 +7532,7 @@ mssql-pyodbc = ["pyodbc"]
 mypy = ["mypy (>=0.910)"]
 mysql = ["mysqlclient (>=1.4.0)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=7)"]
+oracle = ["cx-oracle (>=8)"]
 oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
@@ -7652,7 +7548,6 @@ sqlcipher = ["sqlcipher3-binary"]
 name = "sqlalchemy-utils"
 version = "0.38.3"
 description = "Various utility functions for SQLAlchemy."
-category = "main"
 optional = false
 python-versions = "~=3.6"
 files = [
@@ -7681,7 +7576,6 @@ url = ["furl (>=0.4.1)"]
 name = "sqlite-fts4"
 version = "1.0.3"
 description = "Python functions for working with SQLite FTS4 search"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -7696,7 +7590,6 @@ test = ["pytest"]
 name = "sqlite-migrate"
 version = "0.1b0"
 description = "A simple database migration system for SQLite, based on sqlite-utils"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -7712,19 +7605,18 @@ test = ["black", "mypy", "pytest", "ruff"]
 
 [[package]]
 name = "sqlite-utils"
-version = "3.35"
+version = "3.35.2"
 description = "CLI tool and Python library for manipulating SQLite databases"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "sqlite-utils-3.35.tar.gz", hash = "sha256:8f6fe7f8d12772cd5cf4594703a98dcd0c37c0fd6820dd20541ba74b9fca363a"},
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+    {file = "sqlite-utils-3.35.2.tar.gz", hash = "sha256:590b14ad277914cb3fc7d5e254764847facdaaa23c7bafd85ec93874f6f42143"},
+    {file = "sqlite_utils-3.35.2-py3-none-any.whl", hash = "sha256:afd7df2d248adb9a107695ad73a9abf39b1a4913a80e6915f696ca7420d42a16"},
 ]
 
 [package.dependencies]
 click = "*"
-click-default-group-wheel = "*"
+click-default-group = ">=1.2.3"
 pluggy = "*"
 python-dateutil = "*"
 sqlite-fts4 = "*"
@@ -7739,14 +7631,13 @@ tui = ["trogon"]
 
 [[package]]
 name = "sssom"
-version = "0.3.40"
+version = "0.3.41"
 description = "Operations on SSSOM mapping tables"
-category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
-    {file = "sssom-0.3.40-py3-none-any.whl", hash = "sha256:0aba579aafb329a443bb30b8398a9542368901de0514773c72f018d5948ac206"},
-    {file = "sssom-0.3.40.tar.gz", hash = "sha256:fedba8961593048dc9d78ee44c79c0d5567f52dc0b3382eb80731269a5df3696"},
+    {file = "sssom-0.3.41-py3-none-any.whl", hash = "sha256:04ce1935b3492019b16b7b748c49af366f84bbd3c059982af992d049f46098e7"},
+    {file = "sssom-0.3.41.tar.gz", hash = "sha256:1d09fa9f88153963372811af829ebc1e5aefff935a4e6e12bcb65c94181aa730"},
 ]
 
 [package.dependencies]
@@ -7769,7 +7660,6 @@ validators = ">=0.20.0"
 name = "sssom-schema"
 version = "0.15.0"
 description = "SSSOM is a Simple Standard for Sharing Ontology Mappings."
-category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
@@ -7783,14 +7673,13 @@ mkdocs-mermaid2-plugin = ">=0.6.0,<0.7.0"
 
 [[package]]
 name = "stack-data"
-version = "0.6.2"
+version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
-    {file = "stack_data-0.6.2-py3-none-any.whl", hash = "sha256:cbb2a53eb64e5785878201a97ed7c7b94883f48b87bfb0bbe8b623c74679e4a8"},
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+    {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
+    {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
 ]
 
 [package.dependencies]
@@ -7805,7 +7694,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 name = "starlette"
 version = "0.27.0"
 description = "The little ASGI library that shines."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7822,41 +7710,40 @@ full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart", "pyyam
 
 [[package]]
 name = "streamlit"
-version = "1.26.0"
+version = "1.22.0"
 description = "A faster way to build and share data apps"
-category = "main"
-optional = false
-python-versions = ">=3.8, !=3.9.7"
-files = [
-    {file = "streamlit-1.26.0-py2.py3-none-any.whl", hash = "sha256:2bfdac041816e2e1ba27f061d40112afe61e0d4e72d25f354b38ba81107b4cb3"},
-    {file = "streamlit-1.26.0.tar.gz", hash = "sha256:25475fb15a3cc9fb184945f3fc936f011998bd8386e0c892febe14c9625bf47a"},
-]
-
-[package.dependencies]
-altair = ">=4.0,<6"
-blinker = ">=1.0.0,<2"
-cachetools = ">=4.0,<6"
-click = ">=7.0,<9"
-gitpython = ">=3.0.7,<3.1.19 || >3.1.19,<4"
-importlib-metadata = ">=1.4,<7"
-numpy = ">=1.19.3,<2"
-packaging = ">=16.8,<24"
-pandas = ">=1.3.0,<3"
-pillow = ">=7.1.0,<10"
-protobuf = ">=3.20,<5"
-pyarrow = ">=6.0"
-pydeck = ">=0.8,<1"
-pympler = ">=0.9,<2"
-python-dateutil = ">=2.7.3,<3"
-requests = ">=2.18,<3"
-rich = ">=10.14.0,<14"
-tenacity = ">=8.1.0,<9"
-toml = ">=0.10.1,<2"
-tornado = ">=6.0.3,<7"
-typing-extensions = ">=4.1.0,<5"
-tzlocal = ">=1.1,<5"
-validators = ">=0.2,<1"
-watchdog = {version = ">=2.1.5", markers = "platform_system != \"Darwin\""}
+optional = false
+python-versions = ">=3.7, !=3.9.7"
+files = [
+    {file = "streamlit-1.22.0-py2.py3-none-any.whl", hash = "sha256:520dd9b9e6efb559b5a9a22feadb48b1e6f0340ec83da3514810059fdecd4167"},
+    {file = "streamlit-1.22.0.tar.gz", hash = "sha256:5bef9bf8deef32814d9565c9df48331e6357eb0b90dabc3ec4f53c44fb34fc73"},
+]
+
+[package.dependencies]
+altair = ">=3.2.0,<5"
+blinker = ">=1.0.0"
+cachetools = ">=4.0"
+click = ">=7.0"
+gitpython = "!=3.1.19"
+importlib-metadata = ">=1.4"
+numpy = "*"
+packaging = ">=14.1"
+pandas = ">=0.25,<3"
+pillow = ">=6.2.0"
+protobuf = ">=3.12,<4"
+pyarrow = ">=4.0"
+pydeck = ">=0.1.dev5"
+pympler = ">=0.9"
+python-dateutil = "*"
+requests = ">=2.4"
+rich = ">=10.11.0"
+tenacity = ">=8.0.0,<9"
+toml = "*"
+tornado = ">=6.0.3"
+typing-extensions = ">=3.10.0.0"
+tzlocal = ">=1.1"
+validators = ">=0.2"
+watchdog = {version = "*", markers = "platform_system != \"Darwin\""}
 
 [package.extras]
 snowflake = ["snowflake-snowpark-python"]
@@ -7865,7 +7752,6 @@ snowflake = ["snowflake-snowpark-python"]
 name = "sympy"
 version = "1.12"
 description = "Computer algebra system (CAS) in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -7880,7 +7766,6 @@ mpmath = ">=0.19"
 name = "tabulate"
 version = "0.9.0"
 description = "Pretty-print tabular data"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7895,7 +7780,6 @@ widechars = ["wcwidth"]
 name = "tenacity"
 version = "8.2.3"
 description = "Retry code until it succeeds"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -7908,14 +7792,13 @@ doc = ["reno", "sphinx", "tornado (>=4.5)"]
 
 [[package]]
 name = "terminado"
-version = "0.17.1"
+version = "0.18.0"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "terminado-0.17.1-py3-none-any.whl", hash = "sha256:8650d44334eba354dd591129ca3124a6ba42c3d5b70df5051b6921d506fdaeae"},
-    {file = "terminado-0.17.1.tar.gz", hash = "sha256:6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333"},
+    {file = "terminado-0.18.0-py3-none-any.whl", hash = "sha256:87b0d96642d0fe5f5abd7783857b9cab167f221a39ff98e3b9619a788a3c0f2e"},
+    {file = "terminado-0.18.0.tar.gz", hash = "sha256:1ea08a89b835dd1b8c0c900d92848147cef2537243361b2e3f4dc15df9b6fded"},
 ]
 
 [package.dependencies]
@@ -7926,12 +7809,12 @@ tornado = ">=6.1.0"
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
+typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
 [[package]]
 name = "textract"
 version = "1.5.0"
 description = "extract text from any document. no muss. no fuss."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -7953,7 +7836,6 @@ xlrd = "*"
 name = "threadpoolctl"
 version = "3.2.0"
 description = "threadpoolctl"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -7965,7 +7847,6 @@ files = [
 name = "tiktoken"
 version = "0.4.0"
 description = "tiktoken is a fast BPE tokeniser for use with OpenAI's models"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -8011,7 +7892,6 @@ blobfile = ["blobfile (>=2)"]
 name = "tinycss2"
 version = "1.2.1"
 description = "A tiny CSS parser"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -8028,64 +7908,123 @@ test = ["flake8", "isort", "pytest"]
 
 [[package]]
 name = "tokenizers"
-version = "0.13.3"
-description = "Fast and Customizable Tokenizers"
-category = "main"
+version = "0.15.0"
+description = ""
 optional = false
-python-versions = "*"
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 description = "A lil' TOML parser"
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 optional = false
 python-versions = ">=3.7"
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 version = "0.12.0"
 description = "List processing tools and functional utilities"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
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 typing-extensions = "*"
 
 [package.extras]
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 opt-einsum = ["opt-einsum (>=3.3)"]
 
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 ]
 
 [package.dependencies]
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 requests = "*"
-torch = "2.0.1"
+torch = "2.1.1"
 
 [package.extras]
 scipy = ["scipy"]
 
 [[package]]
 name = "tornado"
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 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
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 optional = false
 python-versions = ">= 3.8"
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 ]
 
 [[package]]
 name = "tox"
-version = "4.10.0"
+version = "4.11.4"
 description = "tox is a generic virtualenv management and test command line tool"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 cachetools = ">=5.3.1"
 chardet = ">=5.2"
 colorama = ">=0.4.6"
-filelock = ">=3.12.2"
+filelock = ">=3.12.3"
 packaging = ">=23.1"
 platformdirs = ">=3.10"
-pluggy = ">=1.2"
-pyproject-api = ">=1.5.3"
+pluggy = ">=1.3"
+pyproject-api = ">=1.6.1"
 tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
 virtualenv = ">=20.24.3"
 
 [package.extras]
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+testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.1.1)", "devpi-process (>=1)", "diff-cover (>=7.7)", "distlib (>=0.3.7)", "flaky (>=3.7)", "hatch-vcs (>=0.3)", "hatchling (>=1.18)", "psutil (>=5.9.5)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-xdist (>=3.3.1)", "re-assert (>=1.1)", "time-machine (>=2.12)", "wheel (>=0.41.2)"]
 
 [[package]]
 name = "tqdm"
 version = "4.66.1"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -8268,58 +8214,55 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.9.0"
+version = "5.14.0"
 description = "Traitlets Python configuration system"
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
-test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "transformers"
-version = "4.32.0"
+version = "4.35.2"
 description = "State-of-the-art Machine Learning for JAX, PyTorch and TensorFlow"
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 ]
 
 [package.dependencies]
 filelock = "*"
-huggingface-hub = ">=0.15.1,<1.0"
+huggingface-hub = ">=0.16.4,<1.0"
 numpy = ">=1.17"
 packaging = ">=20.0"
 pyyaml = ">=5.1"
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 requests = "*"
 safetensors = ">=0.3.1"
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 tqdm = ">=4.27"
 
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 accelerate = ["accelerate (>=0.20.3)"]
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+docs = ["Pillow (<10.0.0)", "accelerate (>=0.20.3)", "av (==9.2.0)", "codecarbon (==1.2.0)", "decord (==0.6.0)", "flax (>=0.4.1,<=0.7.0)", "hf-doc-builder", "jax (>=0.4.1,<=0.4.13)", "jaxlib (>=0.4.1,<=0.4.13)", "kenlm", "keras-nlp (>=0.3.1)", "librosa", "onnxconverter-common", "optax (>=0.0.8,<=0.1.4)", "optuna", "phonemizer", "protobuf", "pyctcdecode (>=0.4.0)", "ray[tune]", "sentencepiece (>=0.1.91,!=0.1.92)", "sigopt", "tensorflow (>=2.6,<2.15)", "tensorflow-text (<2.15)", "tf2onnx", "timm", "tokenizers (>=0.14,<0.19)", "torch (>=1.10,!=1.12.0)", "torchaudio", "torchvision"]
 docs-specific = ["hf-doc-builder"]
-fairscale = ["fairscale (>0.3)"]
 flax = ["flax (>=0.4.1,<=0.7.0)", "jax (>=0.4.1,<=0.4.13)", "jaxlib (>=0.4.1,<=0.4.13)", "optax (>=0.0.8,<=0.1.4)"]
 flax-speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)"]
 ftfy = ["ftfy"]
@@ -8339,29 +8282,28 @@ serving = ["fastapi", "pydantic (<2)", "starlette", "uvicorn"]
 sigopt = ["sigopt"]
 sklearn = ["scikit-learn"]
 speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)", "torchaudio"]
-testing = ["GitPython (<3.1.19)", "beautifulsoup4", "black (>=23.1,<24.0)", "cookiecutter (==1.7.3)", "datasets (!=2.5.0)", "dill (<0.3.5)", "evaluate (>=0.2.0)", "faiss-cpu", "hf-doc-builder (>=0.3.0)", "nltk", "parameterized", "protobuf", "psutil", "pytest (>=7.2.0)", "pytest-timeout", "pytest-xdist", "rjieba", "rouge-score (!=0.0.7,!=0.0.8,!=0.1,!=0.1.1)", "sacrebleu (>=1.4.12,<2.0.0)", "sacremoses", "timeout-decorator"]
-tf = ["keras-nlp (>=0.3.1)", "onnxconverter-common", "tensorflow (>=2.6,<2.14)", "tensorflow-text (<2.14)", "tf2onnx"]
-tf-cpu = ["keras-nlp (>=0.3.1)", "onnxconverter-common", "tensorflow-cpu (>=2.6,<2.14)", "tensorflow-text (<2.14)", "tf2onnx"]
+testing = ["GitPython (<3.1.19)", "beautifulsoup4", "black (>=23.1,<24.0)", "cookiecutter (==1.7.3)", "datasets (!=2.5.0)", "dill (<0.3.5)", "evaluate (>=0.2.0)", "faiss-cpu", "hf-doc-builder (>=0.3.0)", "nltk", "parameterized", "protobuf", "psutil", "pytest (>=7.2.0)", "pytest-timeout", "pytest-xdist", "rjieba", "rouge-score (!=0.0.7,!=0.0.8,!=0.1,!=0.1.1)", "sacrebleu (>=1.4.12,<2.0.0)", "sacremoses", "tensorboard", "timeout-decorator"]
+tf = ["keras-nlp (>=0.3.1)", "onnxconverter-common", "tensorflow (>=2.6,<2.15)", "tensorflow-text (<2.15)", "tf2onnx"]
+tf-cpu = ["keras-nlp (>=0.3.1)", "onnxconverter-common", "tensorflow-cpu (>=2.6,<2.15)", "tensorflow-text (<2.15)", "tf2onnx"]
 tf-speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)"]
 timm = ["timm"]
-tokenizers = ["tokenizers (>=0.11.1,!=0.11.3,<0.14)"]
-torch = ["accelerate (>=0.20.3)", "torch (>=1.9,!=1.12.0)"]
+tokenizers = ["tokenizers (>=0.14,<0.19)"]
+torch = ["accelerate (>=0.20.3)", "torch (>=1.10,!=1.12.0)"]
 torch-speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)", "torchaudio"]
 torch-vision = ["Pillow (<10.0.0)", "torchvision"]
-torchhub = ["filelock", "huggingface-hub (>=0.15.1,<1.0)", "importlib-metadata", "numpy (>=1.17)", "packaging (>=20.0)", "protobuf", "regex (!=2019.12.17)", "requests", "sentencepiece (>=0.1.91,!=0.1.92)", "tokenizers (>=0.11.1,!=0.11.3,<0.14)", "torch (>=1.9,!=1.12.0)", "tqdm (>=4.27)"]
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 video = ["av (==9.2.0)", "decord (==0.6.0)"]
 vision = ["Pillow (<10.0.0)"]
 
 [[package]]
 name = "trio"
-version = "0.22.2"
+version = "0.23.1"
 description = "A friendly Python library for async concurrency and I/O"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "trio-0.22.2-py3-none-any.whl", hash = "sha256:f43da357620e5872b3d940a2e3589aa251fd3f881b65a608d742e00809b1ec38"},
-    {file = "trio-0.22.2.tar.gz", hash = "sha256:3887cf18c8bcc894433420305468388dac76932e9668afa1c49aa3806b6accb3"},
+    {file = "trio-0.23.1-py3-none-any.whl", hash = "sha256:bb4abb3f4af23f96679e7c8cdabb8b234520f2498550d2cf63ebfd95f2ce27fe"},
+    {file = "trio-0.23.1.tar.gz", hash = "sha256:16f89f7dcc8f7b9dcdec1fcd863e0c039af6d0f9a22f8dfd56f75d75ec73fd48"},
 ]
 
 [package.dependencies]
@@ -8370,31 +8312,54 @@ cffi = {version = ">=1.14", markers = "os_name == \"nt\" and implementation_name
 exceptiongroup = {version = ">=1.0.0rc9", markers = "python_version < \"3.11\""}
 idna = "*"
 outcome = "*"
-sniffio = "*"
+sniffio = ">=1.3.0"
 sortedcontainers = "*"
 
 [[package]]
 name = "trio-websocket"
-version = "0.10.3"
+version = "0.11.1"
 description = "WebSocket library for Trio"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "trio-websocket-0.10.3.tar.gz", hash = "sha256:1a748604ad906a7dcab9a43c6eb5681e37de4793ba0847ef0bc9486933ed027b"},
-    {file = "trio_websocket-0.10.3-py3-none-any.whl", hash = "sha256:a9937d48e8132ebf833019efde2a52ca82d223a30a7ea3e8d60a7d28f75a4e3a"},
+    {file = "trio-websocket-0.11.1.tar.gz", hash = "sha256:18c11793647703c158b1f6e62de638acada927344d534e3c7628eedcb746839f"},
+    {file = "trio_websocket-0.11.1-py3-none-any.whl", hash = "sha256:520d046b0d030cf970b8b2b2e00c4c2245b3807853ecd44214acd33d74581638"},
 ]
 
 [package.dependencies]
-exceptiongroup = "*"
+exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 trio = ">=0.11"
 wsproto = ">=0.14"
 
+[[package]]
+name = "triton"
+version = "2.1.0"
+description = "A language and compiler for custom Deep Learning operations"
+optional = false
+python-versions = "*"
+files = [
+    {file = "triton-2.1.0-0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:66439923a30d5d48399b08a9eae10370f6c261a5ec864a64983bae63152d39d7"},
+    {file = "triton-2.1.0-0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:919b06453f0033ea52c13eaf7833de0e57db3178d23d4e04f9fc71c4f2c32bf8"},
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+]
+
+[package.dependencies]
+filelock = "*"
+
+[package.extras]
+build = ["cmake (>=3.18)", "lit"]
+tests = ["autopep8", "flake8", "isort", "numpy", "pytest", "scipy (>=1.7.1)"]
+tutorials = ["matplotlib", "pandas", "tabulate"]
+
 [[package]]
 name = "typer"
 version = "0.9.0"
 description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -8412,23 +8377,32 @@ dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2
 doc = ["cairosvg (>=2.5.2,<3.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pillow (>=9.3.0,<10.0.0)"]
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+[[package]]
+name = "types-python-dateutil"
+version = "2.8.19.14"
+description = "Typing stubs for python-dateutil"
+optional = false
+python-versions = "*"
+files = [
+    {file = "types-python-dateutil-2.8.19.14.tar.gz", hash = "sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b"},
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+]
+
 [[package]]
 name = "typing-extensions"
-version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.7+"
-category = "main"
+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 = [
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 [[package]]
 name = "tzdata"
 version = "2023.3"
 description = "Provider of IANA time zone data"
-category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -8438,28 +8412,25 @@ files = [
 
 [[package]]
 name = "tzlocal"
-version = "4.3.1"
+version = "5.2"
 description = "tzinfo object for the local timezone"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "tzlocal-5.2.tar.gz", hash = "sha256:8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e"},
 ]
 
 [package.dependencies]
-pytz-deprecation-shim = "*"
 tzdata = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-devenv = ["black", "check-manifest", "flake8", "pyroma", "pytest (>=4.3)", "pytest-cov", "pytest-mock (>=3.3)", "zest.releaser"]
+devenv = ["check-manifest", "pytest (>=4.3)", "pytest-cov", "pytest-mock (>=3.3)", "zest.releaser"]
 
 [[package]]
 name = "uri-template"
 version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -8474,7 +8445,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 name = "uritemplate"
 version = "4.1.1"
 description = "Implementation of RFC 6570 URI Templates"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -8486,7 +8456,6 @@ files = [
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 description = "URL normalization for Python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -8499,34 +8468,32 @@ six = "*"
 
 [[package]]
 name = "urllib3"
-version = "1.26.16"
+version = "1.26.18"
 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.*"
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 [package.dependencies]
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 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
 secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "uvicorn"
-version = "0.23.2"
+version = "0.24.0.post1"
 description = "The lightning-fast ASGI server."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -8537,7 +8504,7 @@ httptools = {version = ">=0.5.0", optional = true, markers = "extra == \"standar
 python-dotenv = {version = ">=0.13", optional = true, markers = "extra == \"standard\""}
 pyyaml = {version = ">=5.1", optional = true, markers = "extra == \"standard\""}
 typing-extensions = {version = ">=4.0", markers = "python_version < \"3.11\""}
-uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "sys_platform != \"win32\" and sys_platform != \"cygwin\" and platform_python_implementation != \"PyPy\" and extra == \"standard\""}
+uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "(sys_platform != \"win32\" and sys_platform != \"cygwin\") and platform_python_implementation != \"PyPy\" and extra == \"standard\""}
 watchfiles = {version = ">=0.13", optional = true, markers = "extra == \"standard\""}
 websockets = {version = ">=10.4", optional = true, markers = "extra == \"standard\""}
 
@@ -8546,97 +8513,94 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)",
 
 [[package]]
 name = "uvloop"
-version = "0.17.0"
+version = "0.19.0"
 description = "Fast implementation of asyncio event loop on top of libuv"
-category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8.0"
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@@ -8674,34 +8638,86 @@ watchmedo = ["PyYAML (>=3.10)"]
 
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 [package.dependencies]
@@ -8709,21 +8725,19 @@ anyio = ">=3.0.0"
 
 [[package]]
 name = "wcwidth"
-version = "0.2.6"
+version = "0.2.12"
 description = "Measures the displayed width of unicode strings in a terminal"
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 version = "1.13"
 description = "A library for working with the color formats defined by HTML and CSS."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 name = "webencodings"
 version = "0.5.1"
 description = "Character encoding aliases for legacy web content"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -8749,14 +8762,13 @@ files = [
 
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 name = "websocket-client"
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 description = "WebSocket client for Python with low level API options"
-category = "main"
 optional = false
 python-versions = ">=3.8"
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 [package.extras]
@@ -8766,101 +8778,100 @@ test = ["websockets"]
 
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+version = "12.0"
 description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)"
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 version = "1.2.0"
 description = "WebSockets state-machine based protocol implementation"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -8975,7 +8979,6 @@ h11 = ">=0.9.0,<1"
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 version = "2.0.1"
 description = "Library for developers to extract data from Microsoft Excel (tm) .xls spreadsheet files"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -8990,21 +8993,19 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
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 description = "Makes working with XML feel like you are working with JSON"
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 optional = false
 python-versions = ">=3.4"
 files = [
@@ -9014,86 +9015,101 @@ files = [
 
 [[package]]
 name = "yarl"
-version = "1.9.2"
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+    {file = "yarl-1.9.3-py3-none-any.whl", hash = "sha256:271d63396460b6607b588555ea27a1a02b717ca2e3f2cf53bdde4013d7790929"},
+    {file = "yarl-1.9.3.tar.gz", hash = "sha256:4a14907b597ec55740f63e52d7fee0e9ee09d5b9d57a4f399a7423268e457b57"},
 ]
 
 [package.dependencies]
@@ -9102,18 +9118,17 @@ multidict = ">=4.0"
 
 [[package]]
 name = "zipp"
-version = "3.16.2"
+version = "3.17.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
-    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "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"]
 testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [extras]
@@ -9123,4 +9138,4 @@ docs = []
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9, !=3.9.7"
-content-hash = "694d344657ea61dee29d922193ca0c8b45197cd18313997a5acf25c92f568189"
+content-hash = "a14543acbc6a4fa778cfa989851cdacbef240790fc996a32facc1b24a3812ad5"
diff --git a/pyproject.toml b/pyproject.toml
index 5f4e58c..336f326 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.9, !=3.9.7"
-click = "*"
+click = "^8.1.7"
 importlib-metadata = ">=6"
 oaklib = ">=0.5.15"
 beautifulsoup4 = ">=4.8.0"
@@ -46,10 +46,13 @@ llm = "^0.12"
 llm-gpt4all = "^0.1.1"
 gspread = "^5.10.0"
 defusedxml = "^0.7.1"
+click-default-group = "^1.2.4"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=7.1.2"
 tox = ">=3.25.1"
+linkml = "^1.5.6"
+jupyter = "^1.0.0"
 sphinx = {version = ">=6.1.3", extras = ["docs"]}
 sphinx-rtd-theme = {version = ">=1.0.0", extras = ["docs"]}
 sphinx-autodoc-typehints = {version = ">=1.2.0", extras = ["docs"]}
@@ -72,9 +75,6 @@ docs = [
 bioc = [
     "bioc"
 ]
-[tool.poetry.group.dev.dependencies]
-linkml = "^1.5.6"
-jupyter = "^1.0.0"
 
 [tool.poetry-dynamic-versioning]
 enable = false
@@ -85,6 +85,40 @@ style = "pep440"
 line-length = 100
 target-version = ["py38", "py39", "py310"]
 
+[tool.ruff]
+extend-ignore = [
+    "D211",  # `no-blank-line-before-class`
+    "D212",  # `multi-line-summary-first-line`
+    ]
+line-length = 100
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+
+# Select or ignore from https://beta.ruff.rs/docs/rules/
+select = [
+    # "B",  # bugbear
+    # "D",  # pydocstyle
+    # "E",  # pycodestyle errors
+    "F",  # Pyflakes
+    "I",  # isort
+    # "S",  # flake8-bandit
+    "W",  # Warning
+]
+
+unfixable = []
+target-version = "py310"
+
+[tool.ruff.mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 10
+
+[tool.codespell]
+skip = "*.po,*.ts,.git,pyproject.toml"
+count = ""
+quiet-level = 3
+# ignore-words-list = ""
+
 [tool.isort]
 profile = "black"
 multi_line_output = 3
diff --git a/src/curate_gpt/__init__.py b/src/curate_gpt/__init__.py
index ce75fb8..9584f35 100644
--- a/src/curate_gpt/__init__.py
+++ b/src/curate_gpt/__init__.py
@@ -1,4 +1,5 @@
-"""CurateGPT: A framework semi-assisted curation of knowledge bases.
+"""
+CurateGPT: A framework semi-assisted curation of knowledge bases.
 
 Architecture
 ============
diff --git a/src/curate_gpt/agents/__init__.py b/src/curate_gpt/agents/__init__.py
index 1ac0d82..862dd92 100644
--- a/src/curate_gpt/agents/__init__.py
+++ b/src/curate_gpt/agents/__init__.py
@@ -1,4 +1,5 @@
-"""CurateGPT Agents.
+"""
+CurateGPT Agents.
 
 These chain together different search and generate components.
 """
diff --git a/src/curate_gpt/agents/agent_utils.py b/src/curate_gpt/agents/agent_utils.py
index 319a091..395f35a 100644
--- a/src/curate_gpt/agents/agent_utils.py
+++ b/src/curate_gpt/agents/agent_utils.py
@@ -1,3 +1,4 @@
+"""Agent Utilities."""
 import logging
 from typing import Dict, List, Optional, Tuple
 
diff --git a/src/curate_gpt/agents/base_agent.py b/src/curate_gpt/agents/base_agent.py
index 5907ad7..151ed91 100644
--- a/src/curate_gpt/agents/base_agent.py
+++ b/src/curate_gpt/agents/base_agent.py
@@ -1,3 +1,4 @@
+"""Base Agent."""
 from abc import ABC
 from dataclasses import dataclass
 from typing import Union
@@ -8,6 +9,7 @@
 
 @dataclass
 class BaseAgent(ABC):
+
     """
     Base class for agents.
 
diff --git a/src/curate_gpt/agents/chat_agent.py b/src/curate_gpt/agents/chat_agent.py
index fc2cc74..eb79533 100644
--- a/src/curate_gpt/agents/chat_agent.py
+++ b/src/curate_gpt/agents/chat_agent.py
@@ -16,7 +16,9 @@
 
 
 class ChatResponse(BaseModel):
-    """Response from chat engine.
+
+    """
+    Response from chat engine.
 
     TODO: Rename class to indicate that it is provenance-enabled chat
     """
@@ -38,6 +40,7 @@ class ChatResponse(BaseModel):
 
 
 def replace_references_with_links(text):
+    """Replace references with links."""
     pattern = r"\[(\d+)\]"
     replacement = lambda m: f"[{m.group(1)}](#ref-{m.group(1)})"
     return re.sub(pattern, replacement, text)
@@ -45,6 +48,7 @@ def replace_references_with_links(text):
 
 @dataclass
 class ChatAgent(BaseAgent):
+
     """
     An agent that allows chat to a knowledge source.
 
diff --git a/src/curate_gpt/agents/concept_recognition_agent.py b/src/curate_gpt/agents/concept_recognition_agent.py
index 47d0ee6..6cc9e23 100644
--- a/src/curate_gpt/agents/concept_recognition_agent.py
+++ b/src/curate_gpt/agents/concept_recognition_agent.py
@@ -1,15 +1,12 @@
 """Annotation (Concept Recognition) in texts."""
 import logging
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from enum import Enum
-from typing import Any, ClassVar, Dict, Iterable, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple
 
-import yaml
 from pydantic import BaseModel
 
 from curate_gpt.agents.base_agent import BaseAgent
-from curate_gpt.extract import AnnotatedObject
-from curate_gpt.store import DBAdapter
 
 logger = logging.getLogger(__name__)
 
@@ -18,7 +15,9 @@
 
 
 class Span(BaseModel):
+
     """An individual span of text containing a single concept."""
+
     text: str
 
     start: Optional[int] = None
@@ -33,7 +32,9 @@ class Span(BaseModel):
     is_suspect: bool = False
     """Potential hallucination due to ID/label mismatch."""
 
+
 class GroundingResult(BaseModel):
+
     """Result of grounding text."""
 
     input_text: str
@@ -47,7 +48,9 @@ class GroundingResult(BaseModel):
 
 
 class AnnotationMethod(str, Enum):
+
     """Strategy or algorithm used for CR."""
+
     INLINE = "inline"
     """LLM creates an annotated document"""
 
@@ -59,6 +62,7 @@ class AnnotationMethod(str, Enum):
 
 
 class AnnotatedText(BaseModel):
+
     """In input text annotated with concept instances."""
 
     input_text: str
@@ -153,7 +157,7 @@ def parse_annotations(text, marker_char: str = None) -> List[CONCEPT]:
     :return:
     """
     # First Pass: Extract text within [ ... ]
-    pattern1 = r'\[([^\]]+)\]'
+    pattern1 = r"\[([^\]]+)\]"
     matches = re.findall(pattern1, text)
 
     # Second Pass: Parse the last token of each match
@@ -163,7 +167,7 @@ def parse_annotations(text, marker_char: str = None) -> List[CONCEPT]:
         if marker_char:
             toks = match.split(marker_char)
             if len(toks) > 1:
-                annotation = ' '.join(toks[:-1]).strip()
+                annotation = " ".join(toks[:-1]).strip()
                 id = toks[-1].strip()
             else:
                 annotation = match
@@ -171,7 +175,7 @@ def parse_annotations(text, marker_char: str = None) -> List[CONCEPT]:
         else:
             words = match.split()
             if len(words) > 1 and ":" in words[-1]:
-                annotation = ' '.join(words[:-1])
+                annotation = " ".join(words[:-1])
                 id = words[-1]
             else:
                 annotation = match
@@ -198,14 +202,19 @@ def parse_spans(text: str, concept_dict: Dict[str, str] = None) -> List[Span]:
         concept_label = row[1].strip('"')
         mention_text = ",".join(row[2:])
         verified_concept_label = concept_dict.get(concept_id, None)
-        spans.append(Span(text=mention_text, concept_id=concept_id, concept_label=verified_concept_label,
-                          is_suspect=verified_concept_label != concept_label))
+        spans.append(
+            Span(
+                text=mention_text,
+                concept_id=concept_id,
+                concept_label=verified_concept_label,
+                is_suspect=verified_concept_label != concept_label,
+            )
+        )
     return spans
 
 
 @dataclass
 class ConceptRecognitionAgent(BaseAgent):
-
     identifier_field: str = None
     """Field to use as identifier for objects."""
 
@@ -225,16 +234,17 @@ def ground_concept(
         text: str,
         collection: str = None,
         categories: Optional[List[str]] = None,
-        include_category_in_search = True,
+        include_category_in_search=True,
         context: str = None,
         **kwargs,
     ) -> GroundingResult:
-
         system_prompt = GROUND_PROMPT
         query = text
         if include_category_in_search and categories:
             query += " Categories: " + ", ".join(categories)
-        concept_pairs, concept_prompt = self._label_id_pairs_prompt_section(query, collection, **kwargs)
+        concept_pairs, concept_prompt = self._label_id_pairs_prompt_section(
+            query, collection, **kwargs
+        )
         concept_dict = {c[0]: c[1] for c in concept_pairs}
         system_prompt += concept_prompt
         model = self.extractor.model
@@ -262,9 +272,14 @@ def ground_concept(
                     concept_label = concept_dict[concept_id]
                 else:
                     concept_label = None
-                span = Span(text=text, concept_id=concept_id, concept_label=concept_label, is_suspect=provided_concept_label != concept_label)
+                span = Span(
+                    text=text,
+                    concept_id=concept_id,
+                    concept_label=concept_label,
+                    is_suspect=provided_concept_label != concept_label,
+                )
                 spans.append(span)
-        #spans = parse_spans(response.text(), concept_dict)
+        # spans = parse_spans(response.text(), concept_dict)
         ann = GroundingResult(input_text=text, annotated_text=response.text(), spans=spans)
         return ann
 
@@ -296,12 +311,16 @@ def annotate_two_pass(
         system_prompt = "Your job is to parse the supplied text, identifying instances of concepts "
         if len(categories) == 1:
             system_prompt += f" that represent some kind of {categories[0]}. "
-            system_prompt += ("Mark up the concepts in square brackets, "
-                              "preserving the original text inside the brackets. ")
+            system_prompt += (
+                "Mark up the concepts in square brackets, "
+                "preserving the original text inside the brackets. "
+            )
         else:
             system_prompt += " that represent one of the following categories: "
             system_prompt += ", ".join(categories)
-            system_prompt += "Mark up the concepts in square brackets, with the category after the pipe symbol, "
+            system_prompt += (
+                "Mark up the concepts in square brackets, with the category after the pipe symbol, "
+            )
             system_prompt += "Using the syntax [ORIGINAL TEXT | CATEGORY]."
         logger.debug(f"Prompting with: {text}")
         model = self.extractor.model
@@ -310,12 +329,24 @@ def annotate_two_pass(
         anns = parse_annotations(marked_up_text, "|")
         spans = []
         for term, category in anns:
-            concept = self.ground_concept(term, collection, categories=[category] if category else None, context=text, **kwargs)
+            concept = self.ground_concept(
+                term,
+                collection,
+                categories=[category] if category else None,
+                context=text,
+                **kwargs,
+            )
             if not concept.spans:
                 logger.debug(f"Unable to ground concept {term} in category {category}")
                 continue
             main_span = concept.spans[0]
-            spans.append(Span(text=term, concept_id=main_span.concept_id, concept_label=main_span.concept_label))
+            spans.append(
+                Span(
+                    text=term,
+                    concept_id=main_span.concept_id,
+                    concept_label=main_span.concept_label,
+                )
+            )
         return AnnotatedText(
             input_text=text,
             annotated_text=marked_up_text,
@@ -329,9 +360,10 @@ def annotate_inline(
         categories: List[str] = None,
         **kwargs,
     ) -> AnnotatedText:
-
         system_prompt = ANNOTATE_PROMPT
-        concept_pairs, concepts_prompt = self._label_id_pairs_prompt_section(text, collection, **kwargs)
+        concept_pairs, concepts_prompt = self._label_id_pairs_prompt_section(
+            text, collection, **kwargs
+        )
         concept_dict = {c[0]: c[1] for c in concept_pairs}
         system_prompt += concepts_prompt
         model = self.extractor.model
@@ -339,13 +371,11 @@ def annotate_inline(
         response = model.prompt(text, system=system_prompt)
         anns = parse_annotations(response.text())
         logger.info(f"Anns: {anns}")
-        spans = [Span(text=ann[0], concept_id=ann[1], concept_label=concept_dict.get(ann[1], None)) for ann in anns]
-        return AnnotatedText(
-            input_text=text,
-            spans=spans,
-            annotated_text=response.text()
-        )
-
+        spans = [
+            Span(text=ann[0], concept_id=ann[1], concept_label=concept_dict.get(ann[1], None))
+            for ann in anns
+        ]
+        return AnnotatedText(input_text=text, spans=spans, annotated_text=response.text())
 
     def annotate_concept_list(
         self,
@@ -354,18 +384,28 @@ def annotate_concept_list(
         categories: List[str] = None,
         **kwargs,
     ) -> AnnotatedText:
-
         system_prompt = MENTION_PROMPT
-        concept_pairs, concepts_prompt = self._label_id_pairs_prompt_section(text, collection, **kwargs)
+        concept_pairs, concepts_prompt = self._label_id_pairs_prompt_section(
+            text, collection, **kwargs
+        )
         concept_dict = {c[0]: c[1] for c in concept_pairs}
         system_prompt += concepts_prompt
         model = self.extractor.model
         logger.debug(f"Prompting with: {text}")
         response = model.prompt(text, system=system_prompt)
         spans = parse_spans(response.text(), concept_dict)
-        return AnnotatedText(input_text=text, summary=response.text(), spans=spans, prompt=system_prompt)
+        return AnnotatedText(
+            input_text=text, summary=response.text(), spans=spans, prompt=system_prompt
+        )
 
-    def _label_id_pairs_prompt_section(self, text:str, collection: str, prolog: str = None, relevance_factor: float = None, **kwargs) -> Tuple[List[CONCEPT], str]:
+    def _label_id_pairs_prompt_section(
+        self,
+        text: str,
+        collection: str,
+        prolog: str = None,
+        relevance_factor: float = None,
+        **kwargs,
+    ) -> Tuple[List[CONCEPT], str]:
         prompt = prolog
         if not prompt:
             prompt = "Here are the candidate concepts, as label // ConceptID pairs:\n"
@@ -395,4 +435,4 @@ def _label_id_pairs_prompt_section(self, text:str, collection: str, prolog: str
                 raise ValueError(f"Object {obj} has no label field {label_field}")
             prompt += f"{label} // {id}   \n"
             concept_pairs.append((id, label))
-        return concept_pairs, prompt
\ No newline at end of file
+        return concept_pairs, prompt
diff --git a/src/curate_gpt/agents/dase_agent.py b/src/curate_gpt/agents/dase_agent.py
index 707dce1..24d827e 100644
--- a/src/curate_gpt/agents/dase_agent.py
+++ b/src/curate_gpt/agents/dase_agent.py
@@ -33,6 +33,7 @@ def _dict2str(d: Dict[str, Any]) -> str:
 
 @dataclass
 class DatabaseAugmentedStructuredExtraction(BaseAgent):
+
     """
     Extracts structured objects from unstructured documents.
 
diff --git a/src/curate_gpt/agents/dragon_agent.py b/src/curate_gpt/agents/dragon_agent.py
index 7212a22..834a289 100644
--- a/src/curate_gpt/agents/dragon_agent.py
+++ b/src/curate_gpt/agents/dragon_agent.py
@@ -33,6 +33,7 @@ def _dict2str(d: Dict[str, Any]) -> str:
 
 @dataclass
 class DragonAgent(BaseAgent):
+
     """
     Retrieves objects in response to a query using a structured knowledge source.
 
diff --git a/src/curate_gpt/agents/evidence_agent.py b/src/curate_gpt/agents/evidence_agent.py
index d71781a..f6ab6e7 100644
--- a/src/curate_gpt/agents/evidence_agent.py
+++ b/src/curate_gpt/agents/evidence_agent.py
@@ -9,6 +9,7 @@
 
 @dataclass
 class EvidenceAgent(BaseAgent):
+
     """
     An agent to find evidence for an object by querying a reference source.
 
diff --git a/src/curate_gpt/agents/mapping_agent.py b/src/curate_gpt/agents/mapping_agent.py
index 71b200b..5475871 100644
--- a/src/curate_gpt/agents/mapping_agent.py
+++ b/src/curate_gpt/agents/mapping_agent.py
@@ -5,7 +5,7 @@
 from dataclasses import dataclass
 from enum import Enum
 from random import shuffle
-from typing import Any, Dict, Iterator, List, Optional, Union, Tuple
+from typing import Any, Dict, Iterator, List, Optional, Tuple, Union
 
 import inflection
 import yaml
@@ -43,6 +43,7 @@ class MappingPredicate(str, Enum):
 
 
 class Mapping(BaseModel):
+
     """Response from chat engine."""
 
     subject_id: str
@@ -58,6 +59,7 @@ class MappingSet(BaseModel):
 
 @dataclass
 class MappingAgent(BaseAgent):
+
     """
     An agent to map/align entities.
     """
@@ -191,6 +193,8 @@ def find_links(self, other_collection: str) -> Iterator[Tuple[str, str, str]]:
         :return:
         """
         # TODO
-        for obj, _, info in self.knowledge_source.find(collection=other_collection, include = ["embeddings", "documents", "metadatas"]):
+        for _, _, info in self.knowledge_source.find(
+            collection=other_collection, include=["embeddings", "documents", "metadatas"]
+        ):
             embeddings = info["embeddings"]
             self.knowledge_source.find(embeddings, limit=10)
diff --git a/src/curate_gpt/agents/summarization_agent.py b/src/curate_gpt/agents/summarization_agent.py
index ab4cbec..4afcb11 100644
--- a/src/curate_gpt/agents/summarization_agent.py
+++ b/src/curate_gpt/agents/summarization_agent.py
@@ -1,26 +1,35 @@
 import logging
 from dataclasses import dataclass
-from typing import Dict, Union, List
+from typing import List
 
 from curate_gpt.agents.base_agent import BaseAgent
 from curate_gpt.wrappers import BaseWrapper
 
 logger = logging.getLogger(__name__)
 
+
 @dataclass
 class SummarizationAgent(BaseAgent):
+
     """
     An agent to summarize entities
 
     AKA SPINDOCTOR/TALISMAN
     """
 
-    def summarize(self, object_ids: List[str], description_field: str, name_field: str, strict: bool = False, system_prompt: str = None):
+    def summarize(
+        self,
+        object_ids: List[str],
+        description_field: str,
+        name_field: str,
+        strict: bool = False,
+        system_prompt: str = None,
+    ):
         """
         Summarize a list of objects.
 
         Example:
-
+        -------
         >>> extractor = BasicExtractor()
         >>> wrapper = get_wrapper("alliance_gene")
         >>> agent = SummarizationAgent(wrapper, extractor=extractor)
@@ -48,9 +57,13 @@ def summarize(self, object_ids: List[str], description_field: str, name_field: s
         if isinstance(knowledge_source, BaseWrapper):
             object_iter = knowledge_source.objects(self.knowledge_source_collection, object_ids)
         else:
-            object_iter = knowledge_source.lookup_multiple(object_ids, collection=self.knowledge_source_collection)
+            object_iter = knowledge_source.lookup_multiple(
+                object_ids, collection=self.knowledge_source_collection
+            )
         objects = list(object_iter)
-        descriptions = [(obj.get(name_field, ""), obj.get(description_field, None)) for obj in objects]
+        descriptions = [
+            (obj.get(name_field, ""), obj.get(description_field, None)) for obj in objects
+        ]
         if any(desc[0] is None for desc in descriptions):
             raise ValueError(f"Missing name for objects: {objects}")
         if strict:
diff --git a/src/curate_gpt/app/app.py b/src/curate_gpt/app/app.py
index 71e6aa2..35c838f 100644
--- a/src/curate_gpt/app/app.py
+++ b/src/curate_gpt/app/app.py
@@ -11,8 +11,8 @@
 from curate_gpt import BasicExtractor
 from curate_gpt.agents import MappingAgent
 from curate_gpt.agents.chat_agent import ChatAgent, ChatResponse
-from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.agents.dase_agent import DatabaseAugmentedStructuredExtraction
+from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.agents.evidence_agent import EvidenceAgent
 from curate_gpt.app.components import (
     DimensionalityReductionOptions,
@@ -289,7 +289,7 @@ def html_table(rows: List[dict]) -> str:
         help="Enter label of concept to match.",
     )
     relevant_fields = st.text_input(
-        "Relavant fields",
+        "Relevant fields",
         help="Comma-separated (e.g. label, definition).",
     )
     limit = st.slider(
diff --git a/src/curate_gpt/app/cart.py b/src/curate_gpt/app/cart.py
index f66d8e6..55f781f 100644
--- a/src/curate_gpt/app/cart.py
+++ b/src/curate_gpt/app/cart.py
@@ -4,6 +4,7 @@
 
 
 class CartItem(BaseModel):
+
     """
     A cart item is a single item in a cart
     """
@@ -15,6 +16,7 @@ class CartItem(BaseModel):
 
 
 class Cart(BaseModel):
+
     """
     A cart is a list of items that can be added to or removed from
     """
diff --git a/src/curate_gpt/cli.py b/src/curate_gpt/cli.py
index b09217d..e80308f 100644
--- a/src/curate_gpt/cli.py
+++ b/src/curate_gpt/cli.py
@@ -5,13 +5,13 @@
 import logging
 import sys
 from pathlib import Path
-from typing import Dict, List, Union, Any
+from typing import Any, Dict, List, Union
 
 import click
 import pandas as pd
 import yaml
 from click_default_group import DefaultGroup
-from linkml_runtime.dumpers import yaml_dumper, json_dumper
+from linkml_runtime.dumpers import json_dumper
 from linkml_runtime.utils.yamlutils import YAMLRoot
 from llm import UnknownModelError, get_model, get_plugins
 from llm.cli import load_conversation
@@ -20,9 +20,9 @@
 
 from curate_gpt import ChromaDBAdapter, __version__
 from curate_gpt.agents.chat_agent import ChatAgent, ChatResponse
-from curate_gpt.agents.concept_recognition_agent import ConceptRecognitionAgent, AnnotationMethod
-from curate_gpt.agents.dragon_agent import DragonAgent
+from curate_gpt.agents.concept_recognition_agent import AnnotationMethod, ConceptRecognitionAgent
 from curate_gpt.agents.dase_agent import DatabaseAugmentedStructuredExtraction
+from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.agents.evidence_agent import EvidenceAgent
 from curate_gpt.agents.summarization_agent import SummarizationAgent
 from curate_gpt.evaluation.dae_evaluator import DatabaseAugmentedCompletionEvaluator
@@ -60,19 +60,22 @@ def dump(obj: Union[str, AnnotatedObject, Dict], format="yaml") -> None:
     if isinstance(obj, YAMLRoot):
         obj = json_dumper.to_dict(obj)
     if format is None or format == "yaml":
-        ser = yaml.dump(obj, sort_keys=False)
+        set = yaml.dump(obj, sort_keys=False)
     elif format == "json":
-        ser = json.dumps(obj, indent=2)
+        set = json.dumps(obj, indent=2)
     elif format == "blob":
-        ser = list(obj.values())[0]
+        set = list(obj.values())[0]
     else:
         raise ValueError(f"Unknown format {format}")
-    print(ser)
+    print(set)
+
 
 # logger = logging.getLogger(__name__)
 
 path_option = click.option("-p", "--path", help="Path to a file or directory for database.")
-model_option = click.option("-m", "--model", help="Model to use for generation or embedding, e.g. gpt-4.")
+model_option = click.option(
+    "-m", "--model", help="Model to use for generation or embedding, e.g. gpt-4."
+)
 schema_option = click.option("-s", "--schema", help="Path to schema.")
 collection_option = click.option("-c", "--collection", help="Collection within the database.")
 output_format_option = click.option(
@@ -116,7 +119,7 @@ def dump(obj: Union[str, AnnotatedObject, Dict], format="yaml") -> None:
 init_with_option = click.option(
     "--init-with",
     "-I",
-    help="YAML string for initialzation of main wrapper object.",
+    help="YAML string for initialization of main wrapper object.",
 )
 batch_size_option = click.option(
     "--batch-size", default=None, show_default=True, type=click.INT, help="Batch size for indexing."
@@ -153,7 +156,8 @@ def show_chat_response(response: ChatResponse, show_references: bool = True):
 @click.option("-q", "--quiet")
 @click.version_option(__version__)
 def main(verbose: int, quiet: bool):
-    """CLI for curate-gpt.
+    """
+    CLI for curate-gpt.
 
     :param verbose: Verbosity while running.
     :param quiet: Boolean to be quiet or verbose.
@@ -208,10 +212,11 @@ def index(
     collect,
     **kwargs,
 ):
-    """Index files.
+    """
+    Index files.
 
     Example:
-
+    -------
         curategpt index  -c doc files/*json
 
     """
@@ -323,15 +328,26 @@ def search(query, path, collection, show_documents, **kwargs):
     multiple=True,
     help="Field to show from right collection.",
 )
-
 @output_format_option
-def all_by_all(path, collection, other_collection, other_path, threshold, ids_only, output_format, left_field, right_field, **kwargs):
+def all_by_all(
+    path,
+    collection,
+    other_collection,
+    other_path,
+    threshold,
+    ids_only,
+    output_format,
+    left_field,
+    right_field,
+    **kwargs,
+):
     """Match two collections."""
     db = ChromaDBAdapter(path)
     if other_path is None:
         other_path = path
     other_db = ChromaDBAdapter(other_path)
     results = match_collections(db, collection, other_collection, other_db)
+
     def _obj(obj: Dict, is_left=False) -> Any:
         if ids_only:
             obj = {"id": obj["id"]}
@@ -342,6 +358,7 @@ def _obj(obj: Dict, is_left=False) -> Any:
         side = "left" if is_left else "right"
         obj = {f"{side}_{k}": v for k, v in obj.items()}
         return obj
+
     i = 0
     for obj1, obj2, sim in results:
         if threshold and sim < threshold:
@@ -362,6 +379,7 @@ def _obj(obj: Dict, is_left=False) -> Any:
         dump(obj1, output_format)
         dump(obj2, output_format)
 
+
 @main.command()
 @path_option
 @collection_option
@@ -395,9 +413,7 @@ def matches(id, path, collection):
     "-L",
     help="Field to use as label (defaults to label).",
 )
-@click.option(
-    "-l", "--limit", default=50, show_default=True, help="Number of candidate terms."
-)
+@click.option("-l", "--limit", default=50, show_default=True, help="Number of candidate terms.")
 @click.option(
     "--input-file",
     "-i",
@@ -430,9 +446,20 @@ def matches(id, path, collection):
     multiple=True,
     help="Category/ies for candidate IDs.",
 )
-
 @click.argument("texts", nargs=-1)
-def annotate(texts, path, model, collection, input_file, split_sentences, category, prefix, identifier_field, label_field, **kwargs):
+def annotate(
+    texts,
+    path,
+    model,
+    collection,
+    input_file,
+    split_sentences,
+    category,
+    prefix,
+    identifier_field,
+    label_field,
+    **kwargs,
+):
     """Concept recognition."""
     db = ChromaDBAdapter(path)
     extractor = BasicExtractor()
@@ -458,7 +485,8 @@ def annotate(texts, path, model, collection, input_file, split_sentences, catego
     for text in texts:
         ao = cr.annotate(text, collection=collection, categories=categories, **kwargs)
         dump(ao)
-        print(f"---\n")
+        print("---\n")
+
 
 @main.command()
 @path_option
@@ -672,10 +700,11 @@ def complete(
     output_format,
     **kwargs,
 ):
-    """Generate an entry from a query using object completion.
+    """
+    Generate an entry from a query using object completion.
 
     Example:
-
+    -------
         curategpt generate  -c obo_go "umbelliferose biosynthetic process"
 
     If the string looks like yaml (if it has a ':') then it will be parsed as yaml.
@@ -751,10 +780,11 @@ def complete_multiple(
     output_format,
     **kwargs,
 ):
-    """Generate an entry from a query using object completion for multiple objects.
+    """
+    Generate an entry from a query using object completion for multiple objects.
 
     Example:
-
+    -------
         curategpt generate  -c obo_go terms.txt
     """
     db = ChromaDBAdapter(path)
@@ -784,6 +814,7 @@ def complete_multiple(
             print("---")
             dump(ao.object, format=output_format)
 
+
 @main.command()
 @path_option
 @collection_option
@@ -840,10 +871,11 @@ def complete_all(
     id_file,
     **kwargs,
 ):
-    """Generate missing values for all objects
+    """
+    Generate missing values for all objects
 
     Example:
-
+    -------
         curategpt generate  -c obo_go TODO
     """
     db = ChromaDBAdapter(path)
@@ -938,10 +970,11 @@ def generate_evaluate(
     rule: List[str],
     **kwargs,
 ):
-    """Evaluate generate using a test set.
+    """
+    Evaluate generate using a test set.
 
     Example:
-
+    -------
         curategpt -v generate-evaluate -c cdr_training -T cdr_test -F statements -m gpt-4
     """
     db = ChromaDBAdapter(path)
@@ -1034,10 +1067,11 @@ def evaluate(
     collection,
     **kwargs,
 ):
-    """Evaluate given a task configuration.
+    """
+    Evaluate given a task configuration.
 
     Example:
-
+    -------
         curategpt evaluate src/curate_gpt/conf/tasks/bio-ont.tasks.yaml
     """
     normalized_tasks = []
@@ -1266,18 +1300,19 @@ def citeseek(query, path, collection, model, show_references, _continue, convers
 @collection_option
 @path_option
 @model_option
-@click.option("--view", "-V",  help="Name of the wrapper to use.")
+@click.option("--view", "-V", help="Name of the wrapper to use.")
 @click.option("--name-field", help="Field for names.")
 @click.option("--description-field", help="Field for names.")
 @click.option("--system-prompt", help="System gpt prompt to use.")
 @click.argument("ids", nargs=-1)
 def summarize(ids, path, collection, model, view, **kwargs):
-    """Summarize a list of objects.
+    """
+    Summarize a list of objects.
 
     Retrieves objects by ID from a knowledge source or wrapper and summarizes them.
 
     Example:
-
+    -------
       curategpt summarize --model llama-2-7b-chat -V alliance_gene \
         --name-field symbol --description-field automatedGeneSynopsis \
         --system-prompt "What functions do these genes share?" \
@@ -1448,7 +1483,7 @@ def split_collection(
     Split a collection into test/train/validation.
 
     Example:
-
+    -------
         curategpt -v collections split -c hp --num-training 10 --num-testing 20
 
     The above populates 2 new collections: hp_training and hp_testing.
@@ -1505,10 +1540,11 @@ def ontology():
 )
 @click.argument("ont")
 def index_ontology_command(ont, path, collection, append, model, index_fields, branches, **kwargs):
-    """Index an ontology.
+    """
+    Index an ontology.
 
     Example:
-
+    -------
         curategpt index-ontology  -c obo_hp $db/hp.db
 
     """
@@ -1543,10 +1579,11 @@ def view():
 @click.option("--source-locator")
 @init_with_option
 def view_objects(view, init_with, **kwargs):
-    """View objects in a virtual store.
+    """
+    View objects in a virtual store.
 
     Example:
-
+    -------
         curategpt view objects -V filesystem --init-with "root_directory: /path/to/data"
 
     """
@@ -1566,11 +1603,14 @@ def view_objects(view, init_with, **kwargs):
 @output_format_option
 @click.argument("input_file")
 def unwrap_objects(input_file, view, path, collection, output_format, **kwargs):
-    """Unwrap objects back to source schema.
+    """
+    Unwrap objects back to source schema.
 
     Example:
+    -------
 
-        TODO
+    Todo:
+    ----
 
     """
     vstore = get_wrapper(view, **kwargs)
@@ -1582,7 +1622,6 @@ def unwrap_objects(input_file, view, path, collection, output_format, **kwargs):
         dump(unwrapped, output_format)
 
 
-
 @view.command(name="search")
 @click.option("--view", "-V")
 @click.option("--source-locator")
diff --git a/src/curate_gpt/evaluation/base_evaluator.py b/src/curate_gpt/evaluation/base_evaluator.py
index 069b523..9c070ef 100644
--- a/src/curate_gpt/evaluation/base_evaluator.py
+++ b/src/curate_gpt/evaluation/base_evaluator.py
@@ -8,9 +8,8 @@
 
 @dataclass
 class BaseEvaluator(ABC):
-    """
-    Base class for evaluators.
-    """
+
+    """Base class for evaluators."""
 
     agent: BaseAgent = None
 
diff --git a/src/curate_gpt/evaluation/dae_evaluator.py b/src/curate_gpt/evaluation/dae_evaluator.py
index 6ab9957..47e593a 100644
--- a/src/curate_gpt/evaluation/dae_evaluator.py
+++ b/src/curate_gpt/evaluation/dae_evaluator.py
@@ -19,6 +19,7 @@
 
 @dataclass
 class DatabaseAugmentedCompletionEvaluator(BaseEvaluator):
+
     """
     Retrieves objects in response to a query using a structured knowledge source.
     """
diff --git a/src/curate_gpt/evaluation/evaluation_datamodel.py b/src/curate_gpt/evaluation/evaluation_datamodel.py
index c87df13..fdf4f4c 100644
--- a/src/curate_gpt/evaluation/evaluation_datamodel.py
+++ b/src/curate_gpt/evaluation/evaluation_datamodel.py
@@ -6,6 +6,7 @@
 
 
 class StratifiedCollection(BaseModel):
+
     """
     A collection of objects that have been split into training, test, and validation sets.
     """
@@ -45,6 +46,7 @@ class ClassificationMetrics(BaseModel):
 
 
 class Task(BaseModel):
+
     """
     A task to be run by the evaluation runner.
     """
diff --git a/src/curate_gpt/evaluation/runner.py b/src/curate_gpt/evaluation/runner.py
index 6569afb..cb408af 100644
--- a/src/curate_gpt/evaluation/runner.py
+++ b/src/curate_gpt/evaluation/runner.py
@@ -81,9 +81,7 @@ def run_task(
     task.executed_on = (
         f"{platform.system()}-{platform.release()}-{platform.version()}-{platform.machine()}"
     )
-    agent = DragonAgent(
-        knowledge_source=tdb, knowledge_source_collection="", extractor=extractor
-    )
+    agent = DragonAgent(knowledge_source=tdb, knowledge_source_collection="", extractor=extractor)
     if task.additional_collections:
         if len(task.additional_collections) > 1:
             raise NotImplementedError("Only one additional collection is supported")
diff --git a/src/curate_gpt/extract/__init__.py b/src/curate_gpt/extract/__init__.py
index 522abb3..7c89b32 100644
--- a/src/curate_gpt/extract/__init__.py
+++ b/src/curate_gpt/extract/__init__.py
@@ -1,4 +1,5 @@
-"""CurateGPT Extractors.
+"""
+CurateGPT Extractors.
 
 These handle connections to (remote or local) LLMs,
 and can also extract structured objects from text.
diff --git a/src/curate_gpt/extract/basic_extractor.py b/src/curate_gpt/extract/basic_extractor.py
index 4f5dcb7..875530b 100644
--- a/src/curate_gpt/extract/basic_extractor.py
+++ b/src/curate_gpt/extract/basic_extractor.py
@@ -6,14 +6,15 @@
 from dataclasses import dataclass
 from typing import List
 
-from .extractor import AnnotatedObject, Extractor
 from ..utils.tokens import estimate_num_tokens, max_tokens_by_model
+from .extractor import AnnotatedObject, Extractor
 
 logger = logging.getLogger(__name__)
 
 
 @dataclass
 class BasicExtractor(Extractor):
+
     """
     Extractor that is purely example driven.
     """
diff --git a/src/curate_gpt/extract/extractor.py b/src/curate_gpt/extract/extractor.py
index 608ade0..02469c7 100644
--- a/src/curate_gpt/extract/extractor.py
+++ b/src/curate_gpt/extract/extractor.py
@@ -15,6 +15,7 @@
 
 
 class AnnotatedObject(BaseModel):
+
     """
     Annotated object shadows a basic dictionary object
     """
diff --git a/src/curate_gpt/extract/openai_extractor.py b/src/curate_gpt/extract/openai_extractor.py
index f31dd3d..3546f60 100644
--- a/src/curate_gpt/extract/openai_extractor.py
+++ b/src/curate_gpt/extract/openai_extractor.py
@@ -16,6 +16,7 @@
 
 @dataclass
 class OpenAIExtractor(Extractor):
+
     """
     Extractor that uses OpenAI functions.
     """
diff --git a/src/curate_gpt/extract/recursive_extractor.py b/src/curate_gpt/extract/recursive_extractor.py
index 98d8a40..628834c 100644
--- a/src/curate_gpt/extract/recursive_extractor.py
+++ b/src/curate_gpt/extract/recursive_extractor.py
@@ -12,6 +12,7 @@
 
 @dataclass
 class RecursiveExtractor(Extractor):
+
     """
     Extractor that recursively extracts objects from text.
 
diff --git a/src/curate_gpt/formatters/__init__.py b/src/curate_gpt/formatters/__init__.py
index dcee7b7..d00a6f0 100644
--- a/src/curate_gpt/formatters/__init__.py
+++ b/src/curate_gpt/formatters/__init__.py
@@ -1,4 +1,5 @@
-"""Formats data objects for presentation to humans and machine agents.
+"""
+Formats data objects for presentation to humans and machine agents.
 
 Note: this package is not in heavy use just now.
 
diff --git a/src/curate_gpt/store/__init__.py b/src/curate_gpt/store/__init__.py
index 321f294..e7a949b 100644
--- a/src/curate_gpt/store/__init__.py
+++ b/src/curate_gpt/store/__init__.py
@@ -1,4 +1,5 @@
-"""Adapters for different document stores.
+"""
+Adapters for different document stores.
 
 * Base class: :class:`DBAdapter`
 
diff --git a/src/curate_gpt/store/chromadb_adapter.py b/src/curate_gpt/store/chromadb_adapter.py
index 89e7430..d88fa8b 100644
--- a/src/curate_gpt/store/chromadb_adapter.py
+++ b/src/curate_gpt/store/chromadb_adapter.py
@@ -8,7 +8,8 @@
 
 import chromadb
 import yaml
-from chromadb import ClientAPI as API, Settings
+from chromadb import ClientAPI as API
+from chromadb import Settings
 from chromadb.api import EmbeddingFunction
 from chromadb.types import Collection
 from chromadb.utils import embedding_functions
@@ -32,6 +33,7 @@
 
 @dataclass
 class ChromaDBAdapter(DBAdapter):
+
     """
     An Adapter that wraps a ChromaDB client
     """
@@ -315,7 +317,7 @@ def update_collection_metadata(self, collection_name: str, **kwargs) -> Collecti
                     raise ValueError(f"Cannot change model from {prev_model} to {metadata.model}")
                 else:
                     logger.info(
-                        f"Changing (empy collection) model from {prev_model} to {metadata.model}"
+                        f"Changing (empty collection) model from {prev_model} to {metadata.model}"
                     )
         # self.set_collection_metadata(collection_name=collection_name, metadata=metadata)
         if metadata.name:
@@ -431,9 +433,13 @@ def find(
                     f"Empty metadata for item {i} [num: {len(metadatas)}] doc: {documents[i]}"
                 )
                 continue
-            obj = self._unjson(metadatas[i]), 0.0, {
-                "document": documents[i],
-            }
+            obj = (
+                self._unjson(metadatas[i]),
+                0.0,
+                {
+                    "document": documents[i],
+                },
+            )
             if embeddings:
                 obj[2]["_embeddings"] = embeddings[i]
             yield obj
@@ -558,7 +564,6 @@ def dump_then_load(self, collection: str = None, target: DBAdapter = None):
             logger.debug(f"Dumping {i} of {len(result['ids'])}")
             batched_obj = {}
             for k in ["ids", "metadatas", "documents", "embeddings"]:
-                batched_obj[k] = result[k][i: i + batch_size]
+                batched_obj[k] = result[k][i : i + batch_size]
             target_collection_obj.add(**batched_obj)
             i += batch_size
-
diff --git a/src/curate_gpt/store/db_adapter.py b/src/curate_gpt/store/db_adapter.py
index 9f0a7eb..dd053b4 100644
--- a/src/curate_gpt/store/db_adapter.py
+++ b/src/curate_gpt/store/db_adapter.py
@@ -43,6 +43,7 @@ def _get_file(file: Optional[FILE_LIKE] = None, mode="r") -> Optional[TextIO]:
 
 @dataclass
 class DBAdapter(ABC):
+
     """
     Base class for stores.
 
@@ -140,8 +141,8 @@ def create_view(self, view_name: str, collection: str, expression: QUERY, **kwar
         """
         Create a view in the database.
 
-        TODO
-
+        Todo:
+        ----
         :param view:
         :return:
         """
@@ -317,7 +318,6 @@ def lookup_multiple(self, ids: List[str], **kwargs) -> Iterator[OBJECT]:
         """
         yield from [self.lookup(id, **kwargs) for id in ids]
 
-
     @abstractmethod
     def peek(self, collection: str = None, limit=5, **kwargs) -> Iterator[OBJECT]:
         """
@@ -398,7 +398,7 @@ def dump(
             format = "json"
         if not include:
             include = ["embeddings", "documents", "metadatas"]
-            #include = ["embeddings", "documents", "metadatas"]
+            # include = ["embeddings", "documents", "metadatas"]
         if not isinstance(include, list):
             include = list(include)
         objects = self.find(collection=collection, include=include, **kwargs)
diff --git a/src/curate_gpt/store/in_memory_adapter.py b/src/curate_gpt/store/in_memory_adapter.py
index ca59161..67f6616 100644
--- a/src/curate_gpt/store/in_memory_adapter.py
+++ b/src/curate_gpt/store/in_memory_adapter.py
@@ -34,6 +34,7 @@ def get_collection(self, name: str) -> Collection:
 
 @dataclass
 class InMemoryAdapter(DBAdapter):
+
     """
     Simple in-memory adapter for a object store.
     """
diff --git a/src/curate_gpt/store/metadata.py b/src/curate_gpt/store/metadata.py
index 6958563..d99c673 100644
--- a/src/curate_gpt/store/metadata.py
+++ b/src/curate_gpt/store/metadata.py
@@ -4,6 +4,7 @@
 
 
 class CollectionMetadata(BaseModel):
+
     """
     Metadata about a collection.
 
diff --git a/src/curate_gpt/store/schema_proxy.py b/src/curate_gpt/store/schema_proxy.py
index b18815d..d9860ca 100644
--- a/src/curate_gpt/store/schema_proxy.py
+++ b/src/curate_gpt/store/schema_proxy.py
@@ -9,6 +9,7 @@
 
 @dataclass
 class SchemaProxy:
+
     """
     Manage connection to a schema
     """
diff --git a/src/curate_gpt/utils/search.py b/src/curate_gpt/utils/search.py
index b3e8633..eea436a 100644
--- a/src/curate_gpt/utils/search.py
+++ b/src/curate_gpt/utils/search.py
@@ -1,5 +1,3 @@
 import logging
 
 logger = logging.getLogger(__name__)
-
-
diff --git a/src/curate_gpt/utils/tokens.py b/src/curate_gpt/utils/tokens.py
index 5b73426..1980657 100644
--- a/src/curate_gpt/utils/tokens.py
+++ b/src/curate_gpt/utils/tokens.py
@@ -8,7 +8,8 @@
 
 
 def max_tokens_by_model(model_id: Optional[str] = None):
-    """Return the maximum number of tokens allowed by a model.
+    """
+    Return the maximum number of tokens allowed by a model.
 
     TODO: return precise values, currently an estimate.
     """
@@ -21,7 +22,8 @@ def max_tokens_by_model(model_id: Optional[str] = None):
 
 
 def estimate_num_tokens(messages: List[str], model="gpt-4"):
-    """Return the number of tokens used by a list of messages.
+    """
+    Return the number of tokens used by a list of messages.
 
     Note: this is an estimate
     """
diff --git a/src/curate_gpt/utils/vector_algorithms.py b/src/curate_gpt/utils/vector_algorithms.py
index cef88ae..807ad77 100644
--- a/src/curate_gpt/utils/vector_algorithms.py
+++ b/src/curate_gpt/utils/vector_algorithms.py
@@ -47,7 +47,9 @@ def top_matches(cosine_similarity_matrix: np.ndarray) -> Tuple[np.ndarray, np.nd
     return top_match_indices, top_match_values
 
 
-def top_n_matches(cosine_similarity_matrix: np.ndarray, n: int=10) -> Tuple[np.ndarray, np.ndarray]:
+def top_n_matches(
+    cosine_similarity_matrix: np.ndarray, n: int = 10
+) -> Tuple[np.ndarray, np.ndarray]:
     # Find the indices that would sort each row in descending order
     sorted_indices = np.argsort(-cosine_similarity_matrix, axis=1)
 
@@ -66,16 +68,17 @@ def mmr_diversified_search(
     """
     Perform diversified search using Maximal Marginal Relevance (MMR).
 
-    Parameters:
+    Parameters
+    ----------
     - query_vector: The vector representing the query.
     - document_vectors: The vectors representing the documents.
     - lambda_: Balance parameter between relevance and diversity.
     - top_n: Number of results to return. If None, return all.
 
-    Returns:
+    Returns
+    -------
     - List of indices representing the diversified order of documents.
     """
-
     # If no specific number of results is specified, return all
     if top_n is None:
         top_n = len(document_vectors)
diff --git a/src/curate_gpt/utils/vectordb_operations.py b/src/curate_gpt/utils/vectordb_operations.py
index 2010afe..65cf46d 100644
--- a/src/curate_gpt/utils/vectordb_operations.py
+++ b/src/curate_gpt/utils/vectordb_operations.py
@@ -4,10 +4,12 @@
 from curate_gpt import DBAdapter
 from curate_gpt.utils.vector_algorithms import compute_cosine_similarity, top_matches
 
-
 logger = logging.getLogger(__name__)
 
-def match_collections(db: DBAdapter, left_collection: str, right_collection: str, other_db: DBAdapter=None) -> Iterator[Tuple[dict, dict, float]]:
+
+def match_collections(
+    db: DBAdapter, left_collection: str, right_collection: str, other_db: DBAdapter = None
+) -> Iterator[Tuple[dict, dict, float]]:
     """
     Match every element in left collection with every element in right collection.
 
@@ -30,7 +32,7 @@ def match_collections(db: DBAdapter, left_collection: str, right_collection: str
     right_vectors = [info["_embeddings"] for _, __, info in right_objs]
     logger.info(f"Computing cosine similarity for {len(left_vectors)} x {len(right_vectors)}")
     sim_matrix = compute_cosine_similarity(left_vectors, right_vectors)
-    logger.info(f"Finding top matches")
+    logger.info("Finding top matches")
     tm_ix, tm_vals = top_matches(sim_matrix)
     logger.info(f"Yielding {len(tm_ix)} matches")
     i = 0
diff --git a/src/curate_gpt/views/namer.py b/src/curate_gpt/views/namer.py
index ebe4cc0..c2f01e0 100644
--- a/src/curate_gpt/views/namer.py
+++ b/src/curate_gpt/views/namer.py
@@ -6,6 +6,7 @@
 
 @dataclass
 class Namer:
+
     """
     Maps between opaque IDs and names
 
diff --git a/src/curate_gpt/wrappers/__init__.py b/src/curate_gpt/wrappers/__init__.py
index 3af5a15..8fa6e18 100644
--- a/src/curate_gpt/wrappers/__init__.py
+++ b/src/curate_gpt/wrappers/__init__.py
@@ -1,4 +1,5 @@
-"""Wrappers on top of external data sources.
+"""
+Wrappers on top of external data sources.
 
 Wrappers allow for dynamic or static loading of an external data source
 into a store.
@@ -40,6 +41,11 @@ def get_all_subclasses(cls):
 
 def get_wrapper(name: str, **kwargs) -> BaseWrapper:
     # NOTE: ORDER DEPENDENT. TODO: fix this
+    from curate_gpt.wrappers.bio.alliance_gene_wrapper import AllianceGeneWrapper  # noqa
+    from curate_gpt.wrappers.bio.bacdive_wrapper import BacDiveWrapper  # noqa
+    from curate_gpt.wrappers.bio.gocam_wrapper import GOCAMWrapper  # noqa
+    from curate_gpt.wrappers.bio.mediadive_wrapper import MediaDiveWrapper  # noqa
+    from curate_gpt.wrappers.bio.reactome_wrapper import ReactomeWrapper  # noqa
     from curate_gpt.wrappers.clinical.clinvar_wrapper import ClinVarWrapper  # noqa
     from curate_gpt.wrappers.clinical.hpoa_by_pub_wrapper import HPOAByPubWrapper  # noqa
     from curate_gpt.wrappers.clinical.hpoa_wrapper import HPOAWrapper  # noqa
@@ -50,6 +56,7 @@ def get_wrapper(name: str, **kwargs) -> BaseWrapper:
     from curate_gpt.wrappers.general.gspread_wrapper import GSpreadWrapper  # noqa
     from curate_gpt.wrappers.general.json_wrapper import JSONWrapper  # noqa
     from curate_gpt.wrappers.general.linkml_schema_wrapper import LinkMLSchemarapper  # noqa
+    from curate_gpt.wrappers.investigation.ess_deepdive_wrapper import ESSDeepDiveWrapper  # noqa
     from curate_gpt.wrappers.investigation.ncbi_bioproject_wrapper import (  # noqa
         NCBIBioprojectWrapper,
     )
@@ -57,20 +64,14 @@ def get_wrapper(name: str, **kwargs) -> BaseWrapper:
         NCBIBiosampleWrapper,
     )
     from curate_gpt.wrappers.investigation.nmdc_wrapper import NMDCWrapper  # noqa
-    from curate_gpt.wrappers.investigation.ess_deepdive_wrapper import ESSDeepDiveWrapper  # noqa
+    from curate_gpt.wrappers.legal.reusabledata_wrapper import ReusableDataWrapper  # noqa
     from curate_gpt.wrappers.literature.bioc_wrapper import BiocWrapper  # noqa
     from curate_gpt.wrappers.literature.pmc_wrapper import PMCWrapper  # noqa
     from curate_gpt.wrappers.literature.pubmed_wrapper import PubmedWrapper  # noqa
     from curate_gpt.wrappers.literature.wikipedia_wrapper import WikipediaWrapper  # noqa
     from curate_gpt.wrappers.ontology.bioportal_wrapper import BioportalWrapper  # noqa
-    from curate_gpt.wrappers.ontology.ontology_wrapper import OntologyWrapper  # noqa
     from curate_gpt.wrappers.ontology.oboformat_wrapper import OBOFormatWrapper  # noqa
-    from curate_gpt.wrappers.bio.gocam_wrapper import GOCAMWrapper  # noqa
-    from curate_gpt.wrappers.bio.alliance_gene_wrapper import AllianceGeneWrapper  # noqa
-    from curate_gpt.wrappers.bio.mediadive_wrapper import MediaDiveWrapper  # noqa
-    from curate_gpt.wrappers.bio.bacdive_wrapper import BacDiveWrapper  # noqa
-    from curate_gpt.wrappers.bio.reactome_wrapper import ReactomeWrapper  # noqa
-    from curate_gpt.wrappers.legal.reusabledata_wrapper import ReusableDataWrapper  # noqa
+    from curate_gpt.wrappers.ontology.ontology_wrapper import OntologyWrapper  # noqa
 
     for c in get_all_subclasses(BaseWrapper):
         if c.name == name:
diff --git a/src/curate_gpt/wrappers/base_wrapper.py b/src/curate_gpt/wrappers/base_wrapper.py
index 7a4b9f8..706e0bc 100644
--- a/src/curate_gpt/wrappers/base_wrapper.py
+++ b/src/curate_gpt/wrappers/base_wrapper.py
@@ -17,6 +17,7 @@
 
 @dataclass
 class BaseWrapper(ABC):
+
     """
     A virtual store that implements a view over some remote or external source.
     """
@@ -171,7 +172,7 @@ def split_objects(self, objects: List[Dict], text_field="text", id_field="id") -
                     new_obj[id_field] = f"{obj_id}#{n}"
                     new_obj[text_field] = text[: self.max_text_length + self.text_overlap]
                     new_objects.append(new_obj)
-                    text = text[self.max_text_length:]
+                    text = text[self.max_text_length :]
             else:
                 new_objects.append(obj)
         return new_objects
diff --git a/src/curate_gpt/wrappers/bio/alliance_gene_wrapper.py b/src/curate_gpt/wrappers/bio/alliance_gene_wrapper.py
index 059ac1f..0985e26 100644
--- a/src/curate_gpt/wrappers/bio/alliance_gene_wrapper.py
+++ b/src/curate_gpt/wrappers/bio/alliance_gene_wrapper.py
@@ -1,17 +1,10 @@
 """Chat with a KB."""
-import gzip
-import os
-import requests
 import logging
 from dataclasses import dataclass, field
 from typing import ClassVar, Dict, Iterable, Iterator, Optional
 
 import requests_cache
-from bs4 import BeautifulSoup
-from glob import glob
-
-import yaml
-from oaklib import BasicOntologyInterface, get_adapter
+from oaklib import BasicOntologyInterface
 
 from curate_gpt.wrappers import BaseWrapper
 
@@ -19,8 +12,10 @@
 
 BASE_URL = "https://www.alliancegenome.org/api"
 
+
 @dataclass
 class AllianceGeneWrapper(BaseWrapper):
+
     """
     A wrapper over a Alliance (AGR) gene API.
 
@@ -35,8 +30,7 @@ class AllianceGeneWrapper(BaseWrapper):
 
     taxon_id: str = field(default="NCBITaxon:9606")
 
-
-    def object_ids(self, taxon_id: str=None, **kwargs) -> Iterator[str]:
+    def object_ids(self, taxon_id: str = None, **kwargs) -> Iterator[str]:
         """
         Get all gene ids for a given taxon id
 
@@ -48,10 +42,13 @@ def object_ids(self, taxon_id: str=None, **kwargs) -> Iterator[str]:
 
         if not taxon_id:
             taxon_id = self.taxon_id
-        response = session.get(f"{BASE_URL}/geneMap/geneIDs", params={
-            "taxonID": taxon_id,
-            "rows": 50000,
-        })
+        response = session.get(
+            f"{BASE_URL}/geneMap/geneIDs",
+            params={
+                "taxonID": taxon_id,
+                "rows": 50000,
+            },
+        )
         response.raise_for_status()
         gene_ids = response.text.split(",")
         yield from gene_ids
@@ -82,4 +79,3 @@ def objects(
             response.raise_for_status()
             obj = response.json()
             yield obj
-
diff --git a/src/curate_gpt/wrappers/bio/bacdive_wrapper.py b/src/curate_gpt/wrappers/bio/bacdive_wrapper.py
index b33fb8d..7b29d46 100644
--- a/src/curate_gpt/wrappers/bio/bacdive_wrapper.py
+++ b/src/curate_gpt/wrappers/bio/bacdive_wrapper.py
@@ -4,9 +4,6 @@
 from dataclasses import dataclass
 from typing import ClassVar, Dict, Iterable, Iterator, Optional
 
-import yaml
-from jsonpath_ng import parse
-
 from curate_gpt.wrappers.base_wrapper import BaseWrapper
 
 logger = logging.getLogger(__name__)
@@ -14,6 +11,7 @@
 
 @dataclass
 class BacDiveWrapper(BaseWrapper):
+
     """
     A wrapper over a bacdive json files.
 
@@ -40,7 +38,7 @@ def wrap_object(self, obj: Dict) -> Iterator[Dict]:
         general = obj["General"]
         name_info = obj["Name and taxonomic classification"]
         new_obj = {}
-        new_obj["id"] = self.create_curie(general['BacDive-ID'])
+        new_obj["id"] = self.create_curie(general["BacDive-ID"])
         new_obj["name"] = name_info.get("full scientific name", None)
         if not new_obj["name"]:
             new_obj["name"] = name_info["LPSN"].get("scientific name", None)
@@ -55,4 +53,3 @@ def wrap_object(self, obj: Dict) -> Iterator[Dict]:
                 break
         new_obj = {**new_obj, **obj}
         yield new_obj
-
diff --git a/src/curate_gpt/wrappers/bio/gocam_wrapper.py b/src/curate_gpt/wrappers/bio/gocam_wrapper.py
index 7c38bd0..36cce60 100644
--- a/src/curate_gpt/wrappers/bio/gocam_wrapper.py
+++ b/src/curate_gpt/wrappers/bio/gocam_wrapper.py
@@ -59,6 +59,7 @@ def _annotations(obj: Dict) -> Dict:
 
 @dataclass
 class GOCAMWrapper(BaseWrapper):
+
     """
     An view over a GO CAM source.
     """
diff --git a/src/curate_gpt/wrappers/bio/mediadive_wrapper.py b/src/curate_gpt/wrappers/bio/mediadive_wrapper.py
index 2fbfe39..bd57138 100644
--- a/src/curate_gpt/wrappers/bio/mediadive_wrapper.py
+++ b/src/curate_gpt/wrappers/bio/mediadive_wrapper.py
@@ -1,10 +1,9 @@
 import logging
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import ClassVar, Dict, Iterable, Iterator, Optional
 
 import requests_cache
-
-from oaklib import BasicOntologyInterface, get_adapter
+from oaklib import BasicOntologyInterface
 
 from curate_gpt.wrappers import BaseWrapper
 
@@ -12,8 +11,10 @@
 
 BASE_URL = "https://mediadive.dsmz.de/rest"
 
+
 @dataclass
 class MediaDiveWrapper(BaseWrapper):
+
     """
     A wrapper over MediaDive.
     """
@@ -69,4 +70,3 @@ def objects(
             else:
                 logger.warning(f"No solutions for {object_id}")
             yield obj
-
diff --git a/src/curate_gpt/wrappers/bio/reactome_wrapper.py b/src/curate_gpt/wrappers/bio/reactome_wrapper.py
index 7c07a58..77b919f 100644
--- a/src/curate_gpt/wrappers/bio/reactome_wrapper.py
+++ b/src/curate_gpt/wrappers/bio/reactome_wrapper.py
@@ -1,17 +1,10 @@
 """Chat with a KB."""
-import gzip
-import os
-import requests
 import logging
 from dataclasses import dataclass, field
-from typing import ClassVar, Dict, Iterable, Iterator, Optional, List
+from typing import ClassVar, Dict, Iterable, Iterator, List, Optional
 
 import requests_cache
-from bs4 import BeautifulSoup
-from glob import glob
-
-import yaml
-from oaklib import BasicOntologyInterface, get_adapter
+from oaklib import BasicOntologyInterface
 
 from curate_gpt.wrappers import BaseWrapper
 
@@ -19,6 +12,7 @@
 
 BASE_URL = "https://reactome.org/ContentService/data"
 
+
 def ids_from_tree(objs: List):
     """
     Recursively yield all ids from a tree of objects
@@ -77,6 +71,7 @@ def generic_object(obj: dict):
 
 @dataclass
 class ReactomeWrapper(BaseWrapper):
+
     """
     A wrapper over a Reactome API.
     """
@@ -91,7 +86,7 @@ class ReactomeWrapper(BaseWrapper):
 
     taxon_id: str = field(default="NCBITaxon:9606")
 
-    def object_ids(self, taxon_id: str=None, **kwargs) -> Iterator[str]:
+    def object_ids(self, taxon_id: str = None, **kwargs) -> Iterator[str]:
         """
         Get all object ids for a given taxon id
 
@@ -137,12 +132,13 @@ def objects(
             response = session.get(f"{BASE_URL}/query/{local_id}")
             obj = response.json()
             summations = obj["summation"]
-            new_obj = {"id": object_id,
-                   "label": obj["displayName"],
-                    "speciesName": obj["speciesName"],
-                    "description": "\n".join([x["text"] for x in summations]),
-                   "type": obj["schemaClass"],
-                   }
+            new_obj = {
+                "id": object_id,
+                "label": obj["displayName"],
+                "speciesName": obj["speciesName"],
+                "description": "\n".join([x["text"] for x in summations]),
+                "type": obj["schemaClass"],
+            }
             for key, func in OBJECT_FUNCTION_MAP.items():
                 if key in obj:
                     new_obj[key] = [func(x) for x in obj[key] if isinstance(x, dict)]
diff --git a/src/curate_gpt/wrappers/clinical/clinvar_wrapper.py b/src/curate_gpt/wrappers/clinical/clinvar_wrapper.py
index d0bee87..d5bfde6 100644
--- a/src/curate_gpt/wrappers/clinical/clinvar_wrapper.py
+++ b/src/curate_gpt/wrappers/clinical/clinvar_wrapper.py
@@ -10,6 +10,7 @@
 
 @dataclass
 class ClinVarWrapper(EUtilsWrapper):
+
     """
     A wrapper to provide a search facade over NCBI clinvar.
 
diff --git a/src/curate_gpt/wrappers/clinical/ctgov_wrapper.py b/src/curate_gpt/wrappers/clinical/ctgov_wrapper.py
index 0b4fe02..ed85f6c 100644
--- a/src/curate_gpt/wrappers/clinical/ctgov_wrapper.py
+++ b/src/curate_gpt/wrappers/clinical/ctgov_wrapper.py
@@ -13,6 +13,7 @@
 
 @dataclass
 class ClinicalTrialsWrapper(BaseWrapper):
+
     """
     A wrapper over a clinicaltrials.gov.
 
diff --git a/src/curate_gpt/wrappers/clinical/hpoa_by_pub_wrapper.py b/src/curate_gpt/wrappers/clinical/hpoa_by_pub_wrapper.py
index 79df83a..aae32fb 100644
--- a/src/curate_gpt/wrappers/clinical/hpoa_by_pub_wrapper.py
+++ b/src/curate_gpt/wrappers/clinical/hpoa_by_pub_wrapper.py
@@ -6,6 +6,7 @@
 
 @dataclass
 class HPOAByPubWrapper(HPOAWrapper):
+
     """
     A wrapper over HPOA grouping by publication
     """
diff --git a/src/curate_gpt/wrappers/clinical/hpoa_wrapper.py b/src/curate_gpt/wrappers/clinical/hpoa_wrapper.py
index 731c3c0..db984ae 100644
--- a/src/curate_gpt/wrappers/clinical/hpoa_wrapper.py
+++ b/src/curate_gpt/wrappers/clinical/hpoa_wrapper.py
@@ -49,6 +49,7 @@ def term_label(identifier: str) -> str:
 
 @dataclass
 class HPOAWrapper(BaseWrapper):
+
     """
     A wrapper over HPOA
 
diff --git a/src/curate_gpt/wrappers/clinical/maxoa_wrapper.py b/src/curate_gpt/wrappers/clinical/maxoa_wrapper.py
index c4f0a31..3b16390 100644
--- a/src/curate_gpt/wrappers/clinical/maxoa_wrapper.py
+++ b/src/curate_gpt/wrappers/clinical/maxoa_wrapper.py
@@ -56,6 +56,7 @@ def term_label(identifier: str) -> str:
 
 @dataclass
 class MAXOAWrapper(BaseWrapper):
+
     """
     A wrapper over HPOA
 
diff --git a/src/curate_gpt/wrappers/general/filesystem_wrapper.py b/src/curate_gpt/wrappers/general/filesystem_wrapper.py
index 4f1ab97..132459a 100644
--- a/src/curate_gpt/wrappers/general/filesystem_wrapper.py
+++ b/src/curate_gpt/wrappers/general/filesystem_wrapper.py
@@ -13,6 +13,7 @@
 
 @dataclass
 class FilesystemWrapper(BaseWrapper):
+
     """
     A wrapper over a filesystem.
 
diff --git a/src/curate_gpt/wrappers/general/github_wrapper.py b/src/curate_gpt/wrappers/general/github_wrapper.py
index 3205d4b..7b165dd 100644
--- a/src/curate_gpt/wrappers/general/github_wrapper.py
+++ b/src/curate_gpt/wrappers/general/github_wrapper.py
@@ -47,6 +47,7 @@ def get_token(token: str = None) -> str:
 
 @dataclass
 class GitHubWrapper(BaseWrapper):
+
     """
     A wrapper to provide a search facade over GitHub.
 
diff --git a/src/curate_gpt/wrappers/general/google_drive_wrapper.py b/src/curate_gpt/wrappers/general/google_drive_wrapper.py
index b962c0d..be9bf97 100644
--- a/src/curate_gpt/wrappers/general/google_drive_wrapper.py
+++ b/src/curate_gpt/wrappers/general/google_drive_wrapper.py
@@ -20,6 +20,7 @@
 
 @dataclass
 class GoogleDriveWrapper(BaseWrapper):
+
     """
     A wrapper to provide a search facade over Wikipedia.
 
diff --git a/src/curate_gpt/wrappers/general/gspread_wrapper.py b/src/curate_gpt/wrappers/general/gspread_wrapper.py
index fe8e387..d8341cf 100644
--- a/src/curate_gpt/wrappers/general/gspread_wrapper.py
+++ b/src/curate_gpt/wrappers/general/gspread_wrapper.py
@@ -16,6 +16,7 @@
 
 @dataclass
 class GSpreadWrapper(BaseWrapper):
+
     """
     A wrapper to provide a search facade over gspread layer onto google sheets.
 
diff --git a/src/curate_gpt/wrappers/general/json_wrapper.py b/src/curate_gpt/wrappers/general/json_wrapper.py
index 8f08f9d..0dbb432 100644
--- a/src/curate_gpt/wrappers/general/json_wrapper.py
+++ b/src/curate_gpt/wrappers/general/json_wrapper.py
@@ -14,6 +14,7 @@
 
 @dataclass
 class JSONWrapper(BaseWrapper):
+
     """
     A wrapper over a json (or yaml) document.
 
diff --git a/src/curate_gpt/wrappers/general/linkml_schema_wrapper.py b/src/curate_gpt/wrappers/general/linkml_schema_wrapper.py
index 7a503cf..27cf149 100644
--- a/src/curate_gpt/wrappers/general/linkml_schema_wrapper.py
+++ b/src/curate_gpt/wrappers/general/linkml_schema_wrapper.py
@@ -13,6 +13,7 @@
 
 @dataclass
 class LinkMLSchemarapper(BaseWrapper):
+
     """
     A wrapper over linkml schema documents.
 
diff --git a/src/curate_gpt/wrappers/investigation/ess_deepdive_wrapper.py b/src/curate_gpt/wrappers/investigation/ess_deepdive_wrapper.py
index 583f957..43a75ab 100644
--- a/src/curate_gpt/wrappers/investigation/ess_deepdive_wrapper.py
+++ b/src/curate_gpt/wrappers/investigation/ess_deepdive_wrapper.py
@@ -4,7 +4,6 @@
 from time import sleep
 from typing import ClassVar, Dict, Iterable, Iterator, Optional
 
-import requests
 import requests_cache
 
 from curate_gpt.wrappers import BaseWrapper
@@ -27,7 +26,9 @@ def _get_records_chunk(session: requests_cache.CachedSession, cursor=1, limit=20
         raise ValueError(f"Could not download records from {url}")
 
 
-def get_records(session: requests_cache.CachedSession, cursor=1, limit=200, maximum: int = None) -> Iterator[dict]:
+def get_records(
+    session: requests_cache.CachedSession, cursor=1, limit=200, maximum: int = None
+) -> Iterator[dict]:
     """
     Iterate through all records in ESSDeepDive and download them.
 
@@ -53,6 +54,7 @@ def get_records(session: requests_cache.CachedSession, cursor=1, limit=200, maxi
 
 @dataclass
 class ESSDeepDiveWrapper(BaseWrapper):
+
     """
     A wrapper over the ESSDeepDive API.
     """
@@ -61,7 +63,9 @@ class ESSDeepDiveWrapper(BaseWrapper):
 
     default_object_type = "Class"
 
-    session: requests_cache.CachedSession = field(default_factory=lambda: requests_cache.CachedSession("ess_deepdive"))
+    session: requests_cache.CachedSession = field(
+        default_factory=lambda: requests_cache.CachedSession("ess_deepdive")
+    )
 
     limit: int = field(default=50)
 
diff --git a/src/curate_gpt/wrappers/investigation/ncbi_bioproject_wrapper.py b/src/curate_gpt/wrappers/investigation/ncbi_bioproject_wrapper.py
index c67de9b..d38a05d 100644
--- a/src/curate_gpt/wrappers/investigation/ncbi_bioproject_wrapper.py
+++ b/src/curate_gpt/wrappers/investigation/ncbi_bioproject_wrapper.py
@@ -12,6 +12,7 @@
 
 @dataclass
 class NCBIBioprojectWrapper(EUtilsWrapper):
+
     """
     A wrapper to provide a search facade over NCBI bioproject.
 
diff --git a/src/curate_gpt/wrappers/investigation/ncbi_biosample_wrapper.py b/src/curate_gpt/wrappers/investigation/ncbi_biosample_wrapper.py
index e2ab4e8..1128fb7 100644
--- a/src/curate_gpt/wrappers/investigation/ncbi_biosample_wrapper.py
+++ b/src/curate_gpt/wrappers/investigation/ncbi_biosample_wrapper.py
@@ -10,6 +10,7 @@
 
 @dataclass
 class NCBIBiosampleWrapper(EUtilsWrapper):
+
     """
     A wrapper to provide a search facade over NCBI Biosample.
 
diff --git a/src/curate_gpt/wrappers/investigation/nmdc_wrapper.py b/src/curate_gpt/wrappers/investigation/nmdc_wrapper.py
index c7d0c2f..e41ba82 100644
--- a/src/curate_gpt/wrappers/investigation/nmdc_wrapper.py
+++ b/src/curate_gpt/wrappers/investigation/nmdc_wrapper.py
@@ -52,6 +52,7 @@ def get_samples(cursor=1, limit=200, maximum: int = None) -> Iterator[dict]:
 
 @dataclass
 class NMDCWrapper(BaseWrapper):
+
     """
     A wrapper over the NMDC Biosample API.
     """
diff --git a/src/curate_gpt/wrappers/legal/reusabledata_wrapper.py b/src/curate_gpt/wrappers/legal/reusabledata_wrapper.py
index 970ab0a..779cfb8 100644
--- a/src/curate_gpt/wrappers/legal/reusabledata_wrapper.py
+++ b/src/curate_gpt/wrappers/legal/reusabledata_wrapper.py
@@ -1,17 +1,12 @@
 """Chat with a KB."""
-import gzip
-import os
-import requests
 import logging
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import ClassVar, Dict, Iterable, Iterator, Optional
 
+import requests
 import requests_cache
 from bs4 import BeautifulSoup
-from glob import glob
-
-import yaml
-from oaklib import BasicOntologyInterface, get_adapter
+from oaklib import BasicOntologyInterface
 
 from curate_gpt.wrappers import BaseWrapper
 
@@ -20,6 +15,7 @@
 
 @dataclass
 class ReusableDataWrapper(BaseWrapper):
+
     """
     A wrapper over a reusabledata.org yaml files.
 
@@ -52,7 +48,15 @@ def objects(
             obj_id = obj["id"]
             license_link = obj.get("license-link", None)
             if license_link:
-                if license_link in ["TODO", "https://", "inconsistent", "https://civic.genome.wustl.edu/about", "http://www.supfam.org/about", "ftp://ftp.nextprot.org/pub/README", "ftp://ftp.jcvi.org/pub/data/TIGRFAMs/COPYRIGHT"]:
+                if license_link in [
+                    "TODO",
+                    "https://",
+                    "inconsistent",
+                    "https://civic.genome.wustl.edu/about",
+                    "http://www.supfam.org/about",
+                    "ftp://ftp.nextprot.org/pub/README",
+                    "ftp://ftp.jcvi.org/pub/data/TIGRFAMs/COPYRIGHT",
+                ]:
                     logger.warning(f"base link {license_link} for {obj_id}")
                     continue
                 if license_link.startswith("ftp://"):
@@ -63,8 +67,7 @@ def objects(
                     logger.warning(f"bad link {license_link} for {obj_id}")
                     continue
                 data = response.text
-                soup = BeautifulSoup(data, 'html.parser')
+                soup = BeautifulSoup(data, "html.parser")
                 license_text = soup.get_text()
                 obj["license_text"] = license_text
             yield obj
-
diff --git a/src/curate_gpt/wrappers/literature/bioc_wrapper.py b/src/curate_gpt/wrappers/literature/bioc_wrapper.py
index 483e6cf..8736099 100644
--- a/src/curate_gpt/wrappers/literature/bioc_wrapper.py
+++ b/src/curate_gpt/wrappers/literature/bioc_wrapper.py
@@ -17,6 +17,7 @@
 
 @dataclass
 class BiocWrapper(BaseWrapper):
+
     """
     A wrapper over a bioc source file.
 
diff --git a/src/curate_gpt/wrappers/literature/eutils_wrapper.py b/src/curate_gpt/wrappers/literature/eutils_wrapper.py
index e116dd0..6f86803 100644
--- a/src/curate_gpt/wrappers/literature/eutils_wrapper.py
+++ b/src/curate_gpt/wrappers/literature/eutils_wrapper.py
@@ -20,6 +20,7 @@
 
 @dataclass
 class EUtilsWrapper(BaseWrapper, ABC):
+
     """
     A wrapper to provide a search facade over NCBI Biosample.
 
diff --git a/src/curate_gpt/wrappers/literature/pmc_wrapper.py b/src/curate_gpt/wrappers/literature/pmc_wrapper.py
index 8474ec7..ad74019 100644
--- a/src/curate_gpt/wrappers/literature/pmc_wrapper.py
+++ b/src/curate_gpt/wrappers/literature/pmc_wrapper.py
@@ -12,6 +12,7 @@
 
 @dataclass
 class PMCWrapper(EUtilsWrapper):
+
     """
     A wrapper to provide a search facade over PMC via eutils.
 
diff --git a/src/curate_gpt/wrappers/literature/pubmed_wrapper.py b/src/curate_gpt/wrappers/literature/pubmed_wrapper.py
index a0458fe..dc9e890 100644
--- a/src/curate_gpt/wrappers/literature/pubmed_wrapper.py
+++ b/src/curate_gpt/wrappers/literature/pubmed_wrapper.py
@@ -39,6 +39,7 @@ def extract_text_from_xml(xml_content):
 # TODO: rewrite to subclass EUtilsWrapper
 @dataclass
 class PubmedWrapper(BaseWrapper):
+
     """
     A wrapper to provide a search facade over PubMed.
 
@@ -222,7 +223,7 @@ def fetch_full_text(self, object_id: str) -> Optional[str]:
                     parsed_url = urlparse(download_url)
                     if parsed_url.scheme not in ["http", "https", "ftp"]:
                         continue
-                    urlretrieve(download_url, local_file_path) # noqa S310
+                    urlretrieve(download_url, local_file_path)  # noqa S310
 
                     # Open and extract the tar.gz file
                     with tarfile.open(local_file_path, "r:gz") as tar:
diff --git a/src/curate_gpt/wrappers/literature/wikipedia_wrapper.py b/src/curate_gpt/wrappers/literature/wikipedia_wrapper.py
index 1ce49bb..2bb6c2d 100644
--- a/src/curate_gpt/wrappers/literature/wikipedia_wrapper.py
+++ b/src/curate_gpt/wrappers/literature/wikipedia_wrapper.py
@@ -16,6 +16,7 @@
 
 @dataclass
 class WikipediaWrapper(BaseWrapper):
+
     """
     A wrapper to provide a search facade over Wikipedia.
 
diff --git a/src/curate_gpt/wrappers/ontology/bioportal_wrapper.py b/src/curate_gpt/wrappers/ontology/bioportal_wrapper.py
index b45da64..ad2732d 100644
--- a/src/curate_gpt/wrappers/ontology/bioportal_wrapper.py
+++ b/src/curate_gpt/wrappers/ontology/bioportal_wrapper.py
@@ -7,6 +7,7 @@
 
 @dataclass
 class BioportalWrapper(OntologyWrapper):
+
     """
     A wrapper over the Bioportal API.
 
diff --git a/src/curate_gpt/wrappers/ontology/oboformat_wrapper.py b/src/curate_gpt/wrappers/ontology/oboformat_wrapper.py
index dbdf75d..e5ac29e 100644
--- a/src/curate_gpt/wrappers/ontology/oboformat_wrapper.py
+++ b/src/curate_gpt/wrappers/ontology/oboformat_wrapper.py
@@ -1,27 +1,16 @@
 """Chat with a KB."""
 import logging
-from collections import defaultdict
-from dataclasses import dataclass, field
-from typing import Any, Callable, ClassVar, Dict, Iterable, Iterator, List, Mapping, Optional
-
-import oaklib.datamodels.obograph as og
-from oaklib import BasicOntologyInterface
-from oaklib.datamodels.search import SearchConfiguration
-from oaklib.datamodels.vocabulary import IS_A
-from oaklib.interfaces import OboGraphInterface, SearchInterface
-from oaklib.types import CURIE
-from oaklib.utilities.iterator_utils import chunk
-
-from curate_gpt import DBAdapter
-from curate_gpt.formatters.format_utils import camelify
+from dataclasses import dataclass
+from typing import ClassVar, Dict, Iterable, Iterator, Optional
+
 from curate_gpt.wrappers.base_wrapper import BaseWrapper
-from curate_gpt.wrappers.ontology.ontology import OntologyClass, Relationship
 
 logger = logging.getLogger(__name__)
 
 
 @dataclass
 class OBOFormatWrapper(BaseWrapper):
+
     """
     A wrapper to index ontologies in OBO Format.
 
@@ -42,7 +31,6 @@ def objects(
 
         :return:
         """
-
         path = self.source_locator
 
         with open(path) as file:
diff --git a/src/curate_gpt/wrappers/ontology/ontology.py b/src/curate_gpt/wrappers/ontology/ontology.py
index 1472cbe..51b6a6d 100644
--- a/src/curate_gpt/wrappers/ontology/ontology.py
+++ b/src/curate_gpt/wrappers/ontology/ontology.py
@@ -4,6 +4,7 @@
 
 
 class Relationship(BaseModel):
+
     """
     A relationship to another node.
 
@@ -15,6 +16,7 @@ class Relationship(BaseModel):
 
 
 class OntologyClass(BaseModel, extra=Extra.allow):
+
     """
     An ontology class.
 
@@ -31,6 +33,7 @@ class OntologyClass(BaseModel, extra=Extra.allow):
 
 
 class Ontology(BaseModel):
+
     """
     An ontology.
 
diff --git a/src/curate_gpt/wrappers/ontology/ontology_wrapper.py b/src/curate_gpt/wrappers/ontology/ontology_wrapper.py
index b5794aa..9df3ada 100644
--- a/src/curate_gpt/wrappers/ontology/ontology_wrapper.py
+++ b/src/curate_gpt/wrappers/ontology/ontology_wrapper.py
@@ -22,6 +22,7 @@
 
 @dataclass
 class OntologyWrapper(BaseWrapper):
+
     """
     A wrapper to pull from ontologies using OAK.
 
@@ -184,8 +185,9 @@ def retrieve_shorthand_to_id_from_store(self, store: DBAdapter) -> Mapping[str,
     def unwrap_object(self, obj: Dict[str, Any], store: DBAdapter, **kwargs) -> og.Graph:
         return self.unwrap_objects([obj], store, **kwargs)
 
-
-    def unwrap_objects(self, objs: Iterable[Dict[str, Any]], store: DBAdapter, drop_dangling=False, **kwargs) -> og.GraphDocument:
+    def unwrap_objects(
+        self, objs: Iterable[Dict[str, Any]], store: DBAdapter, drop_dangling=False, **kwargs
+    ) -> og.GraphDocument:
         """
         Convert an object from the store to the view representation.
 
diff --git a/src/llm_gpt4all.py b/src/llm_gpt4all.py
index 3943b67..5efa459 100644
--- a/src/llm_gpt4all.py
+++ b/src/llm_gpt4all.py
@@ -6,11 +6,10 @@
 from typing import List, Optional, Tuple
 
 import httpx
+import llm
 import urllib3
 from gpt4all import GPT4All as _GPT4All
 
-import llm
-
 
 class GPT4All(_GPT4All):
     # Switch verbose default to False
diff --git a/tests/agents/conftest.py b/tests/agents/conftest.py
index f395107..e1b84c6 100644
--- a/tests/agents/conftest.py
+++ b/tests/agents/conftest.py
@@ -1,8 +1,8 @@
 import pytest
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.store import SchemaProxy
 from curate_gpt.wrappers.ontology import ONTOLOGY_MODEL_PATH
+
 from tests import INPUT_DBS
 
 
diff --git a/tests/agents/test_chat.py b/tests/agents/test_chat.py
index 1001ae5..10ee339 100644
--- a/tests/agents/test_chat.py
+++ b/tests/agents/test_chat.py
@@ -1,7 +1,6 @@
 import re
 
 import pytest
-
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.extract import BasicExtractor
 
diff --git a/tests/agents/test_concept_recognizer.py b/tests/agents/test_concept_recognizer.py
index a97eb11..eb47eca 100644
--- a/tests/agents/test_concept_recognizer.py
+++ b/tests/agents/test_concept_recognizer.py
@@ -1,7 +1,6 @@
 import pytest
 import yaml
-
-from curate_gpt.agents.concept_recognition_agent import ConceptRecognitionAgent, AnnotationMethod
+from curate_gpt.agents.concept_recognition_agent import AnnotationMethod, ConceptRecognitionAgent
 from curate_gpt.extract.basic_extractor import BasicExtractor
 
 
@@ -9,33 +8,36 @@
     "text,categories,prefixes,expected",
     [
         (
-                "A metabolic process that results in the breakdown of chemicals in vacuolar structures.",
-                ["BiologicalProcess", "SubcellularStructure"],
-                ["GO"],
-                ["GO:0044237", "GO:0005773"],
+            "A metabolic process that results in the breakdown of chemicals in vacuolar structures.",
+            ["BiologicalProcess", "SubcellularStructure"],
+            ["GO"],
+            ["GO:0044237", "GO:0005773"],
         ),
         (
-                "A metabolic process that results in the breakdown of chemicals in vacuolar structures.",
-                ["BiologicalProcess", "SubcellularStructure"],
-                ["FAKE"],
-                [],
+            "A metabolic process that results in the breakdown of chemicals in vacuolar structures.",
+            ["BiologicalProcess", "SubcellularStructure"],
+            ["FAKE"],
+            [],
         ),
         (
-                "Protoplasm",
-                None,
-                None,
-                ["GO:0005622"],
+            "Protoplasm",
+            None,
+            None,
+            ["GO:0005622"],
         ),
-(
-                "The photosynthetic membrane of plants and algae",
-                ["BiologicalProcess", "SubcellularStructure", "OrganismTaxon"],
-                None,
-                ["GO:0005622"],
+        (
+            "The photosynthetic membrane of plants and algae",
+            ["BiologicalProcess", "SubcellularStructure", "OrganismTaxon"],
+            None,
+            ["GO:0005622"],
         ),
     ],
 )
-@pytest.mark.parametrize("method", [AnnotationMethod.CONCEPT_LIST, AnnotationMethod.CONCEPT_LIST, AnnotationMethod.TWO_PASS])
-def test_concept_recognizer(go_test_chroma_db, text, categories,prefixes, expected, method):
+@pytest.mark.parametrize(
+    "method",
+    [AnnotationMethod.CONCEPT_LIST, AnnotationMethod.CONCEPT_LIST, AnnotationMethod.TWO_PASS],
+)
+def test_concept_recognizer(go_test_chroma_db, text, categories, prefixes, expected, method):
     limit = 50
     if method == AnnotationMethod.TWO_PASS:
         limit = 10
@@ -44,7 +46,9 @@ def test_concept_recognizer(go_test_chroma_db, text, categories,prefixes, expect
     cr.prefixes = prefixes
     cr.identifier_field = "original_id"
     print(f"## METHOD: {method} CATEGORY: {categories} PREFIXES: {prefixes}")
-    ann = cr.annotate(text, collection="terms_go", method=method, categories=categories, limit=limit)
+    ann = cr.annotate(
+        text, collection="terms_go", method=method, categories=categories, limit=limit
+    )
     print("RESULT:")
     print(yaml.dump(ann.dict(), sort_keys=False))
     overlap = len(set(ann.concepts).intersection(set(expected)))
diff --git a/tests/agents/test_dase.py b/tests/agents/test_dase.py
index 8f1da80..9de656e 100644
--- a/tests/agents/test_dase.py
+++ b/tests/agents/test_dase.py
@@ -1,8 +1,7 @@
 import pytest
 import yaml
-
-from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.agents.dase_agent import DatabaseAugmentedStructuredExtraction
+from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.extract.basic_extractor import BasicExtractor
 
 
diff --git a/tests/agents/test_dragon.py b/tests/agents/test_dragon.py
index 5fc0b81..e3a5c10 100644
--- a/tests/agents/test_dragon.py
+++ b/tests/agents/test_dragon.py
@@ -1,6 +1,5 @@
 import pytest
 import yaml
-
 from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.extract.basic_extractor import BasicExtractor
 
diff --git a/tests/agents/test_mapper.py b/tests/agents/test_mapper.py
index d91334f..748a42d 100644
--- a/tests/agents/test_mapper.py
+++ b/tests/agents/test_mapper.py
@@ -1,5 +1,4 @@
 import pytest
-
 from curate_gpt.agents import MappingAgent
 from curate_gpt.agents.mapping_agent import MappingPredicate
 from curate_gpt.extract import BasicExtractor
diff --git a/tests/cli/test_chat_cli.py b/tests/cli/test_chat_cli.py
index d808409..c9a75fa 100644
--- a/tests/cli/test_chat_cli.py
+++ b/tests/cli/test_chat_cli.py
@@ -1,4 +1,5 @@
 from curate_gpt.cli import main
+
 from tests import INPUT_DIR
 
 ONT_DB = str(INPUT_DIR / "go-nucleus.db")
diff --git a/tests/cli/test_store_cli.py b/tests/cli/test_store_cli.py
index 7907db2..2a3d34b 100644
--- a/tests/cli/test_store_cli.py
+++ b/tests/cli/test_store_cli.py
@@ -1,4 +1,5 @@
 from curate_gpt.cli import main
+
 from tests import INPUT_DIR
 
 ONT_DB = str(INPUT_DIR / "go-nucleus.db")
diff --git a/tests/evaluation/conftest.py b/tests/evaluation/conftest.py
index c3724dc..7fc3840 100644
--- a/tests/evaluation/conftest.py
+++ b/tests/evaluation/conftest.py
@@ -1,9 +1,9 @@
 import pytest
-from oaklib import get_adapter
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.store import SchemaProxy
 from curate_gpt.wrappers.ontology import ONTOLOGY_MODEL_PATH, OntologyWrapper
+from oaklib import get_adapter
+
 from tests import INPUT_DBS, INPUT_DIR
 
 
diff --git a/tests/evaluation/test_calculate_statistics.py b/tests/evaluation/test_calculate_statistics.py
index 9aefff8..e566264 100644
--- a/tests/evaluation/test_calculate_statistics.py
+++ b/tests/evaluation/test_calculate_statistics.py
@@ -1,5 +1,4 @@
 import pytest
-
 from curate_gpt.evaluation.calc_statistics import (
     aggregate_metrics,
     calculate_metrics,
diff --git a/tests/evaluation/test_runner.py b/tests/evaluation/test_runner.py
index d0bbd64..202cc53 100644
--- a/tests/evaluation/test_runner.py
+++ b/tests/evaluation/test_runner.py
@@ -1,8 +1,8 @@
 import pytest
 import yaml
-
 from curate_gpt.evaluation.evaluation_datamodel import Task
 from curate_gpt.evaluation.runner import run_task
+
 from tests import OUTPUT_DIR
 
 
diff --git a/tests/extract/test_extractor.py b/tests/extract/test_extractor.py
index 51e2fb8..17c93ee 100644
--- a/tests/extract/test_extractor.py
+++ b/tests/extract/test_extractor.py
@@ -1,14 +1,13 @@
 from typing import List
 
 import pytest
-from linkml_runtime.utils.schema_builder import SchemaBuilder
-from pydantic import BaseModel
-
 from curate_gpt.extract.basic_extractor import BasicExtractor
 from curate_gpt.extract.extractor import AnnotatedObject
 from curate_gpt.extract.openai_extractor import OpenAIExtractor
 from curate_gpt.extract.recursive_extractor import RecursiveExtractor
 from curate_gpt.store.schema_proxy import SchemaProxy
+from linkml_runtime.utils.schema_builder import SchemaBuilder
+from pydantic import BaseModel
 
 
 class Occupation(BaseModel):
@@ -131,7 +130,8 @@ def test_extract(extractor_type, kwargs, num_examples, schema_manager):
     ],
 )
 def test_deserialize(input, output):
-    """Test that the basic extractor can deserialize a json object.
+    """
+    Test that the basic extractor can deserialize a json object.
 
     Ensures that is capable of handling some of the prefixual junk that
     some models provide
diff --git a/tests/input/dbs/go-nucleus-chroma/chroma.sqlite3 b/tests/input/dbs/go-nucleus-chroma/chroma.sqlite3
new file mode 100644
index 0000000..ece9713
Binary files /dev/null and b/tests/input/dbs/go-nucleus-chroma/chroma.sqlite3 differ
diff --git a/tests/store/test_chromadb_adapter.py b/tests/store/test_chromadb_adapter.py
index 4e85f98..6303334 100644
--- a/tests/store/test_chromadb_adapter.py
+++ b/tests/store/test_chromadb_adapter.py
@@ -3,12 +3,12 @@
 
 import pytest
 import yaml
-from linkml_runtime.utils.schema_builder import SchemaBuilder
-from oaklib import get_adapter
-
 from curate_gpt.store.chromadb_adapter import ChromaDBAdapter
 from curate_gpt.store.schema_proxy import SchemaProxy
 from curate_gpt.wrappers.ontology import ONTOLOGY_MODEL_PATH, OntologyWrapper
+from linkml_runtime.utils.schema_builder import SchemaBuilder
+from oaklib import get_adapter
+
 from tests import INPUT_DBS, INPUT_DIR, OUTPUT_CHROMA_DB_PATH, OUTPUT_DIR
 
 EMPTY_DB_PATH = OUTPUT_DIR / "empty_db"
diff --git a/tests/store/test_in_memory_adapter.py b/tests/store/test_in_memory_adapter.py
index bd66ee9..cab48ac 100644
--- a/tests/store/test_in_memory_adapter.py
+++ b/tests/store/test_in_memory_adapter.py
@@ -1,11 +1,11 @@
 from typing import Dict
 
 import pytest
-from linkml_runtime.utils.schema_builder import SchemaBuilder
-
 from curate_gpt import DBAdapter
 from curate_gpt.store import get_store
 from curate_gpt.store.schema_proxy import SchemaProxy
+from linkml_runtime.utils.schema_builder import SchemaBuilder
+
 from tests import OUTPUT_DIR
 
 EMPTY_DB_PATH = OUTPUT_DIR / "empty_db"
diff --git a/tests/utils/test_search.py b/tests/utils/test_search.py
index b9c59c2..c3711d7 100644
--- a/tests/utils/test_search.py
+++ b/tests/utils/test_search.py
@@ -1,7 +1,6 @@
 import numpy as np
 import pytest
-
-from curate_gpt.utils.search import mmr_diversified_search
+from curate_gpt.utils.vector_algorithms import mmr_diversified_search
 
 vectors = np.array(
     [
diff --git a/tests/wrappers/test_bioportal.py b/tests/wrappers/test_bioportal.py
index c9f9a0e..a53780d 100644
--- a/tests/wrappers/test_bioportal.py
+++ b/tests/wrappers/test_bioportal.py
@@ -1,11 +1,11 @@
 import logging
 
 import pytest
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.ontology.bioportal_wrapper import BioportalWrapper
 from curate_gpt.wrappers.ontology.ontology_wrapper import OntologyWrapper
+
 from tests import OUTPUT_DIR
 
 TEMP_OAKVIEW_DB = OUTPUT_DIR / "bioportal_tmp"
diff --git a/tests/wrappers/test_clinvar.py b/tests/wrappers/test_clinvar.py
index f58c735..a8b580d 100644
--- a/tests/wrappers/test_clinvar.py
+++ b/tests/wrappers/test_clinvar.py
@@ -4,12 +4,12 @@
 
 import pytest
 import yaml
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.clinical.clinvar_wrapper import ClinVarWrapper
+
 from tests import INPUT_DIR, OUTPUT_DIR
 
 TEMP_DB = OUTPUT_DIR / "obj_tmp"
diff --git a/tests/wrappers/test_evidence_agent.py b/tests/wrappers/test_evidence_agent.py
index a8bd07a..efaa3bc 100644
--- a/tests/wrappers/test_evidence_agent.py
+++ b/tests/wrappers/test_evidence_agent.py
@@ -4,12 +4,12 @@
 
 import pytest
 import yaml
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.agents.evidence_agent import EvidenceAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers import BaseWrapper
 from curate_gpt.wrappers.literature import PubmedWrapper, WikipediaWrapper
+
 from tests import OUTPUT_DIR
 
 TEMP_PUBMED_DB = OUTPUT_DIR / "pmid_tmp"
diff --git a/tests/wrappers/test_gocam.py b/tests/wrappers/test_gocam.py
index c1d068b..e146edc 100644
--- a/tests/wrappers/test_gocam.py
+++ b/tests/wrappers/test_gocam.py
@@ -2,8 +2,8 @@
 
 import pytest
 import yaml
+from curate_gpt.wrappers.bio.gocam_wrapper import GOCAMWrapper
 
-from curate_gpt.wrappers.sysbio.gocam_wrapper import GOCAMWrapper
 from tests import INPUT_DIR
 
 
diff --git a/tests/wrappers/test_hpoa.py b/tests/wrappers/test_hpoa.py
index 3ea5da8..99ee085 100644
--- a/tests/wrappers/test_hpoa.py
+++ b/tests/wrappers/test_hpoa.py
@@ -2,8 +2,8 @@
 
 import pytest
 import yaml
-
 from curate_gpt.wrappers.clinical.hpoa_wrapper import HPOAWrapper
+
 from tests import INPUT_DIR, OUTPUT_DIR
 
 TEMP_DB = OUTPUT_DIR / "obj_tmp"
diff --git a/tests/wrappers/test_json.py b/tests/wrappers/test_json.py
index df0b0d0..9249db4 100644
--- a/tests/wrappers/test_json.py
+++ b/tests/wrappers/test_json.py
@@ -1,4 +1,5 @@
 from curate_gpt.wrappers import get_wrapper
+
 from tests import INPUT_DIR
 
 
diff --git a/tests/wrappers/test_linkml_schema.py b/tests/wrappers/test_linkml_schema.py
index e8502f0..acff9a7 100644
--- a/tests/wrappers/test_linkml_schema.py
+++ b/tests/wrappers/test_linkml_schema.py
@@ -1,4 +1,5 @@
 from curate_gpt.wrappers import get_wrapper
+
 from tests import INPUT_DIR
 
 
diff --git a/tests/wrappers/test_ncbi_biosample.py b/tests/wrappers/test_ncbi_biosample.py
index 1aaea1d..c7b8d31 100644
--- a/tests/wrappers/test_ncbi_biosample.py
+++ b/tests/wrappers/test_ncbi_biosample.py
@@ -3,11 +3,11 @@
 import time
 
 import yaml
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.investigation.ncbi_biosample_wrapper import NCBIBiosampleWrapper
+
 from tests import OUTPUT_DIR
 
 TEMP_BIOSAMPLE_DB = OUTPUT_DIR / "biosample_tmp"
diff --git a/tests/wrappers/test_ontology.py b/tests/wrappers/test_ontology.py
index 96aba28..6fe0c65 100644
--- a/tests/wrappers/test_ontology.py
+++ b/tests/wrappers/test_ontology.py
@@ -2,11 +2,11 @@
 import shutil
 
 import pytest
-from oaklib import get_adapter
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.ontology.ontology_wrapper import OntologyWrapper
+from oaklib import get_adapter
+
 from tests import INPUT_DIR, OUTPUT_DIR
 
 TEMP_OAKVIEW_DB = OUTPUT_DIR / "oaktmp"
diff --git a/tests/wrappers/test_pmc.py b/tests/wrappers/test_pmc.py
index 4844e9f..c174dd2 100644
--- a/tests/wrappers/test_pmc.py
+++ b/tests/wrappers/test_pmc.py
@@ -4,12 +4,12 @@
 
 import pytest
 import yaml
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.agents.dragon_agent import DragonAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.literature.pmc_wrapper import PMCWrapper
+
 from tests import INPUT_DIR, OUTPUT_DIR
 
 TEMP_DB = OUTPUT_DIR / "obj_tmp"
diff --git a/tests/wrappers/test_pubmed.py b/tests/wrappers/test_pubmed.py
index 64538e9..1f0d155 100644
--- a/tests/wrappers/test_pubmed.py
+++ b/tests/wrappers/test_pubmed.py
@@ -6,6 +6,7 @@
 from curate_gpt.agents.chat_agent import ChatAgent
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.literature import PubmedWrapper
+
 from tests import OUTPUT_DIR
 
 TEMP_PUBMED_DB = OUTPUT_DIR / "pmid_tmp"
diff --git a/tests/wrappers/test_wikipedia.py b/tests/wrappers/test_wikipedia.py
index bf9526a..5e2d372 100644
--- a/tests/wrappers/test_wikipedia.py
+++ b/tests/wrappers/test_wikipedia.py
@@ -3,10 +3,10 @@
 import time
 
 import yaml
-
 from curate_gpt import ChromaDBAdapter
 from curate_gpt.extract import BasicExtractor
 from curate_gpt.wrappers.literature import WikipediaWrapper
+
 from tests import OUTPUT_DIR
 
 TEMP_Wikipedia_DB = OUTPUT_DIR / "wp_tmp"
diff --git a/tox.ini b/tox.ini
index 275c878..8512422 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,86 +4,83 @@
 # and then run "tox" from this directory.
 
 [tox]
-isolated_build = true
+# To use a PEP 517 build-backend you are required to configure tox to use an isolated_build:
+# https://tox.readthedocs.io/en/latest/example/package.html
+isolated_build = True
+skipsdist = True
+
 envlist =
+    # always keep coverage-clean first
+    coverage-clean
+    lint-fix
     lint
-    flake8
+    codespell-write
+    ; docstr-coverage
     py
 
 [testenv]
-# forward env.vars to tox env for tests\test_implementations\test_sqldb.py
-passenv =
-    LNAME
-    LOGNAME
-    USER
-    USERNAME
+allowlist_externals =
+    poetry
 commands =
-    coverage run -p -m pytest --durations=20 {posargs:tests}
-    coverage combine
-    coverage xml
+    poetry run pytest {posargs}
+description = Run unit tests with pytest. This is a special environment that does not get a name, and
+              can be referenced with "py".
+
+[testenv:coverage-clean]
+deps = coverage
+skip_install = true
+commands = coverage erase
+
+# This is used during development
+[testenv:lint-fix]
 deps =
-    pytest
-    coverage
-    semsimian
+    black
+    ruff
+skip_install = true
+commands =
+    black src/ tests/
+    ruff --fix src/ tests/
+description = Run linters.
 
+# This is used for QC checks.
 [testenv:lint]
 deps =
     black
-    isort
+    ruff
 skip_install = true
 commands =
-    black src/curate_gpt tests/
-    isort src/curate_gpt tests/
+    black --check --diff src/ tests/
+    ruff check src/ tests/
 description = Run linters.
 
-[testenv:flake8]
-skip_install = true
+[testenv:doclint]
 deps =
-    flake8<5.0.0
-    flake8-bandit
-    flake8-black
-    flake8-bugbear
-    flake8-colors
-    flake8-isort
-    pep8-naming
+    rstfmt
+skip_install = true
 commands =
-    flake8 src/curate_gpt tests/
-description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming).
+    rstfmt docs/source/
+description = Run documentation linters.
 
-#########################
-# Flake8 Configuration  #
-# (.flake8)             #
-#########################
-[flake8]
-ignore =
-    E203
-    W503
-    C901 # needs code change so ignoring for now.
-    E731 # needs code change so ignoring for now.
-    S101 # asserts are fine
-    S106 # flags false positives with test_table_filler
-    N801 # mixed case is bad but there's a lot of auto-generated code
-    N815 # same ^
-    S404 # Consider possible security implications associated with the subprocess module.
-    S108 # Probable insecure usage of temp file/directory.
-    S307 # Use of possibly insecure function - consider using safer ast.literal_eval.
-    S603 # subprocess call - check for execution of untrusted input.
-    S607 # Starting a process with a partial executable path ["open" in both cases]
-    S608 # Possible SQL injection vector through string-based query construction.
-    B024 # StreamingWriter is an abstract base class, but it has no abstract methods. 
-         # Remember to use @abstractmethod, @abstractclassmethod and/or @abstractproperty decorators.
-    B027 # empty method in an abstract base class, but has no abstract decorator. Consider adding @abstractmethod
-    N803 # math-oriented classes can ignore this (e.g. hypergeometric.py)
-    N806 # math-oriented classes can ignore this (e.g. hypergeometric.py)
-    B019
-    S113 # new check - deal with this later
-    
-max-line-length = 120
-max-complexity = 13
-import-order-style = pycharm
-application-import-names =
-    oaklib
-    tests
-exclude =
-    datamodels   ## datamodels are auto-generated
-    src/curate_gpt/wrappers/__init__.py
+[testenv:codespell]
+description = Run spell checker.
+skip_install = true
+deps =
+    codespell
+    tomli  # required for getting config from pyproject.toml
+commands = codespell src/ tests/
+
+[testenv:codespell-write]
+description = Run spell checker and write corrections.
+skip_install = true
+deps =
+    codespell
+    tomli
+commands = codespell src/ tests/ --write-changes
+
+[testenv:docstr-coverage]
+skip_install = true
+deps =
+    docstr-coverage
+commands =
+    docstr-coverage src/ tests/ --skip-private --skip-magic
+description = Run the docstr-coverage tool to check documentation coverage
\ No newline at end of file