From 4fc381da394d48460a6ee6529381a736d7d66417 Mon Sep 17 00:00:00 2001
From: Saurabh Mogre <saurabh.mogre@alleninstitute.org>
Date: Thu, 17 Oct 2024 12:09:07 -0700
Subject: [PATCH] Update pyproject.toml dependencies and add pdm lock file

---
 pdm.lock       | 2061 ++++++++++++++++++++----------------------------
 pyproject.toml |   90 +--
 2 files changed, 881 insertions(+), 1270 deletions(-)

diff --git a/pdm.lock b/pdm.lock
index 8ec7d5ad..7293795b 100644
--- a/pdm.lock
+++ b/pdm.lock
@@ -2,13 +2,13 @@
 # It is not intended for manual editing.
 
 [metadata]
-groups = ["default"]
+groups = ["default", "dev", "lint", "setup", "test"]
 strategy = ["inherit_metadata"]
 lock_version = "4.5.0"
-content_hash = "sha256:90dc4c2d78229239be242c4043b94a0a9bfe83e37a1a564e0d9a3b9e875631d8"
+content_hash = "sha256:1097f7223c5fa5eb81c6627d1c6b1515ae527f10eff1487c26b1b9477ae3c1ae"
 
 [[metadata.targets]]
-requires_python = ">=3.9"
+requires_python = "==3.9.*"
 
 [[package]]
 name = "aicsimageio"
@@ -64,66 +64,6 @@ dependencies = [
     "yarl<2.0,>=1.12.0",
 ]
 files = [
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-    {file = "aiohttp-3.10.10-cp313-cp313-win32.whl", hash = "sha256:4470c73c12cd9109db8277287d11f9dd98f77fc54155fc71a7738a83ffcc8ea8"},
-    {file = "aiohttp-3.10.10-cp313-cp313-win_amd64.whl", hash = "sha256:486f7aabfa292719a2753c016cc3a8f8172965cabb3ea2e7f7436c7f5a22a151"},
     {file = "aiohttp-3.10.10-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:01948b1d570f83ee7bbf5a60ea2375a89dfb09fd419170e7f5af029510033d24"},
     {file = "aiohttp-3.10.10-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9fc1500fd2a952c5c8e3b29aaf7e3cc6e27e9cfc0a8819b3bce48cc1b849e4cc"},
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@@ -156,6 +96,17 @@ files = [
     {file = "aiosignal-1.3.1.tar.gz", hash = "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc"},
 ]
 
+[[package]]
+name = "alabaster"
+version = "0.7.16"
+requires_python = ">=3.9"
+summary = "A light, configurable Sphinx theme"
+groups = ["dev"]
+files = [
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+]
+
 [[package]]
 name = "annotated-types"
 version = "0.7.0"
@@ -189,6 +140,20 @@ files = [
     {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"},
 ]
 
+[[package]]
+name = "asttokens"
+version = "2.4.1"
+summary = "Annotate AST trees with source code positions"
+groups = ["dev"]
+dependencies = [
+    "six>=1.12.0",
+    "typing; python_version < \"3.5\"",
+]
+files = [
+    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
+    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+]
+
 [[package]]
 name = "async-timeout"
 version = "4.0.3"
@@ -218,25 +183,61 @@ files = [
     {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
+[[package]]
+name = "babel"
+version = "2.16.0"
+requires_python = ">=3.8"
+summary = "Internationalization utilities"
+groups = ["dev"]
+dependencies = [
+    "pytz>=2015.7; python_version < \"3.9\"",
+]
+files = [
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
+]
+
+[[package]]
+name = "black"
+version = "22.12.0"
+requires_python = ">=3.7"
+summary = "The uncompromising code formatter."
+groups = ["lint"]
+dependencies = [
+    "click>=8.0.0",
+    "mypy-extensions>=0.4.3",
+    "pathspec>=0.9.0",
+    "platformdirs>=2",
+    "tomli>=1.1.0; python_full_version < \"3.11.0a7\"",
+    "typed-ast>=1.4.2; python_version < \"3.8\" and implementation_name == \"cpython\"",
+    "typing-extensions>=3.10.0.0; python_version < \"3.10\"",
+]
+files = [
+    {file = "black-22.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:101c69b23df9b44247bd88e1d7e90154336ac4992502d4197bdac35dd7ee3320"},
+    {file = "black-22.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:559c7a1ba9a006226f09e4916060982fd27334ae1998e7a38b3f33a37f7a2148"},
+    {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
+    {file = "black-22.12.0.tar.gz", hash = "sha256:229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f"},
+]
+
 [[package]]
 name = "boto3"
-version = "1.35.41"
+version = "1.35.42"
 requires_python = ">=3.8"
 summary = "The AWS SDK for Python"
 groups = ["default"]
 dependencies = [
-    "botocore<1.36.0,>=1.35.41",
+    "botocore<1.36.0,>=1.35.42",
     "jmespath<2.0.0,>=0.7.1",
     "s3transfer<0.11.0,>=0.10.0",
 ]
 files = [
-    {file = "boto3-1.35.41-py3-none-any.whl", hash = "sha256:2bf7e7f376aee52155fc4ae4487f29333a6bcdf3a05c3bc4fede10b972d951a6"},
-    {file = "boto3-1.35.41.tar.gz", hash = "sha256:e74bc6d69c04ca611b7f58afe08e2ded6cb6504a4a80557b656abeefee395f88"},
+    {file = "boto3-1.35.42-py3-none-any.whl", hash = "sha256:e1f36f8be453505cebcc3da178ea081b2a06c0e5e1cdee774f1067599b8d9c3e"},
+    {file = "boto3-1.35.42.tar.gz", hash = "sha256:a5b00f8b82dce62870759f04861747944da834d64a64355970120c475efdafc0"},
 ]
 
 [[package]]
 name = "botocore"
-version = "1.35.41"
+version = "1.35.42"
 requires_python = ">=3.8"
 summary = "Low-level, data-driven core of boto 3."
 groups = ["default"]
@@ -247,8 +248,19 @@ dependencies = [
     "urllib3<1.27,>=1.25.4; python_version < \"3.10\"",
 ]
 files = [
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+version = "1.0.1"
+requires_python = ">=3.5"
+summary = "Version-bump your software with a single command!"
+groups = ["dev"]
+files = [
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 version = "5.5.0"
 requires_python = ">=3.7"
 summary = "Extensible memoizing collections and decorators"
-groups = ["default"]
+groups = ["default", "dev"]
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 version = "2024.8.30"
 requires_python = ">=3.6"
 summary = "Python package for providing Mozilla's CA Bundle."
-groups = ["default"]
+groups = ["default", "dev"]
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-groups = ["default"]
+groups = ["default", "lint"]
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-groups = ["default"]
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+groups = ["default", "dev"]
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+groups = ["test"]
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+summary = "IPython: Productive Interactive Computing"
+groups = ["dev"]
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+    "decorator",
+    "exceptiongroup; python_version < \"3.11\"",
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+summary = "An autocompletion tool for Python that can be used for text editors."
+groups = ["dev"]
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-groups = ["default"]
+groups = ["default", "dev"]
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+summary = "Inline Matplotlib backend for Jupyter"
+groups = ["dev"]
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@@ -2956,12 +2464,22 @@ name = "six"
 version = "1.16.0"
 requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 summary = "Python 2 and 3 compatibility utilities"
-groups = ["default"]
+groups = ["default", "dev"]
 files = [
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 ]
 
+[[package]]
+name = "snowballstemmer"
+version = "2.2.0"
+summary = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+groups = ["dev"]
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
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+]
+
 [[package]]
 name = "sortedcontainers"
 version = "2.4.0"
@@ -2972,6 +2490,148 @@ files = [
     {file = "sortedcontainers-2.4.0.tar.gz", hash = "sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88"},
 ]
 
+[[package]]
+name = "sphinx"
+version = "7.4.7"
+requires_python = ">=3.9"
+summary = "Python documentation generator"
+groups = ["dev"]
+dependencies = [
+    "Jinja2>=3.1",
+    "Pygments>=2.17",
+    "alabaster~=0.7.14",
+    "babel>=2.13",
+    "colorama>=0.4.6; sys_platform == \"win32\"",
+    "docutils<0.22,>=0.20",
+    "imagesize>=1.3",
+    "importlib-metadata>=6.0; python_version < \"3.10\"",
+    "packaging>=23.0",
+    "requests>=2.30.0",
+    "snowballstemmer>=2.2",
+    "sphinxcontrib-applehelp",
+    "sphinxcontrib-devhelp",
+    "sphinxcontrib-htmlhelp>=2.0.0",
+    "sphinxcontrib-jsmath",
+    "sphinxcontrib-qthelp",
+    "sphinxcontrib-serializinghtml>=1.1.9",
+    "tomli>=2; python_version < \"3.11\"",
+]
+files = [
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+[[package]]
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+requires_python = ">=3.8"
+summary = "Read the Docs theme for Sphinx"
+groups = ["dev"]
+dependencies = [
+    "docutils<0.22,>0.18",
+    "sphinx<9,>=6",
+    "sphinxcontrib-jquery<5,>=4",
+]
+files = [
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+[[package]]
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+requires_python = ">=3.9"
+summary = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+groups = ["dev"]
+files = [
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+summary = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+groups = ["dev"]
+files = [
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+[[package]]
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+requires_python = ">=3.9"
+summary = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+groups = ["dev"]
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+
+[[package]]
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+version = "4.1"
+requires_python = ">=2.7"
+summary = "Extension to include jQuery on newer Sphinx releases"
+groups = ["dev"]
+dependencies = [
+    "Sphinx>=1.8",
+]
+files = [
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+[[package]]
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+version = "1.0.1"
+requires_python = ">=3.5"
+summary = "A sphinx extension which renders display math in HTML via JavaScript"
+groups = ["dev"]
+files = [
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+]
+
+[[package]]
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+version = "2.0.0"
+requires_python = ">=3.9"
+summary = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
+groups = ["dev"]
+files = [
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+]
+
+[[package]]
+name = "sphinxcontrib-serializinghtml"
+version = "2.0.0"
+requires_python = ">=3.9"
+summary = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
+groups = ["dev"]
+files = [
+    {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"},
+    {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"},
+]
+
+[[package]]
+name = "stack-data"
+version = "0.6.3"
+summary = "Extract data from python stack frames and tracebacks for informative displays"
+groups = ["dev"]
+dependencies = [
+    "asttokens>=2.1.0",
+    "executing>=1.2.0",
+    "pure-eval",
+]
+files = [
+    {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]]
 name = "tblib"
 version = "3.0.0"
@@ -3030,6 +2690,18 @@ files = [
     {file = "tifffile-2023.2.28.tar.gz", hash = "sha256:2d2baba8dea6609f553fe61853db9a61f715d60ba3bce6a20b5a1ab72407dfed"},
 ]
 
+[[package]]
+name = "tomli"
+version = "2.0.2"
+requires_python = ">=3.8"
+summary = "A lil' TOML parser"
+groups = ["dev", "lint", "test"]
+marker = "python_version < \"3.11\""
+files = [
+    {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"},
+    {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
+]
+
 [[package]]
 name = "toolz"
 version = "1.0.0"
@@ -3061,6 +2733,45 @@ files = [
     {file = "tornado-6.4.1.tar.gz", hash = "sha256:92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9"},
 ]
 
+[[package]]
+name = "tox"
+version = "4.23.0"
+requires_python = ">=3.8"
+summary = "tox is a generic virtualenv management and test command line tool"
+groups = ["dev"]
+dependencies = [
+    "cachetools>=5.5",
+    "chardet>=5.2",
+    "colorama>=0.4.6",
+    "filelock>=3.16.1",
+    "packaging>=24.1",
+    "platformdirs>=4.3.6",
+    "pluggy>=1.5",
+    "pyproject-api>=1.8",
+    "tomli>=2.0.1; python_version < \"3.11\"",
+    "typing-extensions>=4.12.2; python_version < \"3.11\"",
+    "virtualenv>=20.26.6",
+]
+files = [
+    {file = "tox-4.23.0-py3-none-any.whl", hash = "sha256:46da40afb660e46238c251280eb910bdaf00b390c7557c8e4bb611f422e9db12"},
+    {file = "tox-4.23.0.tar.gz", hash = "sha256:a6bd7d54231d755348d3c3a7b450b5bf6563833716d1299a1619587a1b77a3bf"},
+]
+
+[[package]]
+name = "tox-pdm"
+version = "0.7.2"
+requires_python = ">=3.7"
+summary = "A plugin for tox that utilizes PDM as the package manager and installer"
+groups = ["dev"]
+dependencies = [
+    "tomli; python_version < \"3.11\"",
+    "tox>=4.0",
+]
+files = [
+    {file = "tox_pdm-0.7.2-py3-none-any.whl", hash = "sha256:12f6215416b7acd00a80a9e7128f3dc3e3c89308d60707f5d0a24abdf83ac104"},
+    {file = "tox_pdm-0.7.2.tar.gz", hash = "sha256:a841a7e1e942a71805624703b9a6d286663bd6af79bba6130ba756975c315308"},
+]
+
 [[package]]
 name = "tqdm"
 version = "4.66.5"
@@ -3075,6 +2786,17 @@ files = [
     {file = "tqdm-4.66.5.tar.gz", hash = "sha256:e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad"},
 ]
 
+[[package]]
+name = "traitlets"
+version = "5.14.3"
+requires_python = ">=3.8"
+summary = "Traitlets Python configuration system"
+groups = ["dev"]
+files = [
+    {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
+    {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
+]
+
 [[package]]
 name = "trimesh"
 version = "4.5.0"
@@ -3094,7 +2816,7 @@ name = "typing-extensions"
 version = "4.12.2"
 requires_python = ">=3.8"
 summary = "Backported and Experimental Type Hints for Python 3.8+"
-groups = ["default"]
+groups = ["default", "dev", "lint"]
 files = [
     {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
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@@ -3127,12 +2849,42 @@ name = "urllib3"
 version = "1.26.20"
 requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 summary = "HTTP library with thread-safe connection pooling, file post, and more."
-groups = ["default"]
+groups = ["default", "dev"]
 files = [
     {file = "urllib3-1.26.20-py2.py3-none-any.whl", hash = "sha256:0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e"},
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 ]
 
+[[package]]
+name = "virtualenv"
+version = "20.26.6"
+requires_python = ">=3.7"
+summary = "Virtual Python Environment builder"
+groups = ["dev"]
+dependencies = [
+    "distlib<1,>=0.3.7",
+    "filelock<4,>=3.12.2",
+    "importlib-metadata>=6.6; python_version < \"3.8\"",
+    "platformdirs<5,>=3.9.1",
+]
+files = [
+    {file = "virtualenv-20.26.6-py3-none-any.whl", hash = "sha256:7345cc5b25405607a624d8418154577459c3e0277f5466dd79c49d5e492995f2"},
+    {file = "virtualenv-20.26.6.tar.gz", hash = "sha256:280aede09a2a5c317e409a00102e7077c6432c5a38f0ef938e643805a7ad2c48"},
+]
+
+[[package]]
+name = "wcwidth"
+version = "0.2.13"
+summary = "Measures the displayed width of unicode strings in a terminal"
+groups = ["dev"]
+dependencies = [
+    "backports-functools-lru-cache>=1.2.1; python_version < \"3.2\"",
+]
+files = [
+    {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
+    {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
+]
+
 [[package]]
 name = "werkzeug"
 version = "3.0.4"
@@ -3147,6 +2899,17 @@ files = [
     {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"},
 ]
 
+[[package]]
+name = "wheel"
+version = "0.44.0"
+requires_python = ">=3.8"
+summary = "A built-package format for Python"
+groups = ["dev"]
+files = [
+    {file = "wheel-0.44.0-py3-none-any.whl", hash = "sha256:2376a90c98cc337d18623527a97c31797bd02bad0033d41547043a1cbfbe448f"},
+    {file = "wheel-0.44.0.tar.gz", hash = "sha256:a29c3f2817e95ab89aa4660681ad547c0e9547f20e75b0562fe7723c9a2a9d49"},
+]
+
 [[package]]
 name = "wrapt"
 version = "1.16.0"
@@ -3154,36 +2917,6 @@ requires_python = ">=3.6"
 summary = "Module for decorators, wrappers and monkey patching."
 groups = ["default"]
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 ]
 
 [[package]]
@@ -3382,7 +3051,7 @@ name = "zipp"
 version = "3.20.2"
 requires_python = ">=3.8"
 summary = "Backport of pathlib-compatible object wrapper for zip files"
-groups = ["default"]
+groups = ["default", "dev"]
 marker = "python_version < \"3.12\""
 files = [
     {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
diff --git a/pyproject.toml b/pyproject.toml
index 0a62d4ad..c2c01818 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,3 @@
-[tool.pdm]
-
 [project]
 name = "cellpack"
 version = "1.0.8"
@@ -8,17 +6,17 @@ keywords = ["cellpack"]
 readme = "README.md"
 authors = [
     {name = "Megan Riel-Mehan", email = "meganr@alleninstitute.org"},
+    {name = "Saurabh Mogre", email = "saurabh.mogre@alleninstitute.org"},
+    {name = "Ruge Li", email = "ruge.li@alleninstitute.org"},
 ]
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Developers",
     "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
 ]
-requires-python = ">=3.9"
+requires-python = "==3.9.*"
 dependencies = [
     "aicsimageio>=4.10.0",
     "boto3>=1.28.3",
@@ -29,7 +27,6 @@ dependencies = [
     "mdutils>=1.4.0",
     "moto>=5.0.2",
     "numpy>=1.19.2",
-    "pandas>=1.2.4",
     "plotly>=5.3.1",
     "pycollada>=0.7.1",
     "pymunk>=6.2.0",
@@ -47,96 +44,41 @@ license = {text = "MIT license"}
 [project.urls]
 Homepage = "https://github.com/mesoscope/cellpack"
 
-[project.optional-dependencies]
+[project.scripts]
+analyze = "cellpack.bin.analyze:main"
+convert = "cellpack.bin.simularium_converter:main"
+pack = "cellpack.bin.pack:main"
+upload = "cellpack.bin.upload:main"
+
+[tool.pdm.dev-dependencies]
 setup = [
     "pytest-runner>=5.2",
 ]
 test = [
-    "black>=19.10b0, <=23.0",
-    "flake8-debugger>=3.2.1",
-    "flake8>=3.8.3, <=6.0.0",
     "pytest-cov>=2.9.0",
     "pytest-raises>=0.11",
     "pytest>=5.4.3",
 ]
-dev = [
-    "Sphinx>=3.4.3",
-    "aicsimageio>=4.10.0",
+lint = [
     "black>=19.10b0, <=23.0",
-    "bump2version>=1.0.1",
-    "coverage>=5.1",
     "flake8-debugger>=3.2.1",
     "flake8>=3.8.3, <=6.0.0",
-    "ipython>=7.15.0",
-    "m2r2>=0.2.7",
-    "mdutils>=1.4.0",
-    "pandas>=1.2.4",
-    "pytest-cov>=2.9.0",
-    "pytest-raises>=0.11",
-    "pytest-runner>=5.2",
-    "pytest-runner>=5.2",
-    "pytest>=5.4.3",
-    "scikit-learn>=1.1.3",
-    "seaborn>=0.12.1",
-    "sphinx_rtd_theme>=0.5.1",
-    "tox>=3.15.2",
-    "tqdm>=4.64.1",
-    "twine>=3.1.1",
-    "wheel>=0.34.2",
 ]
-all = [
+dev = [
     "Sphinx>=3.4.3",
-    "aicsimageio>=4.10.0",
-    "aicsimageio>=4.10.0",
-    "black>=19.10b0, <=23.0",
-    "boto3>=1.28.3",
     "bump2version>=1.0.1",
     "coverage>=5.1",
-    "deepdiff>=5.5.0",
-    "fire>=0.4.0",
-    "firebase_admin>=6.0.1",
-    "flake8-debugger>=3.2.1",
-    "flake8>=3.8.3, <=6.0.0",
     "ipython>=7.15.0",
     "m2r2>=0.2.7",
-    "matplotlib>=3.3.4",
-    "mdutils>=1.4.0",
-    "mdutils>=1.4.0",
-    "moto>=5.0.2",
-    "numpy>=1.19.2",
-    "pandas>=1.2.4",
-    "pandas>=1.2.4",
-    "plotly>=5.3.1",
-    "pycollada>=0.7.1",
-    "pymunk>=6.2.0",
-    "pytest-cov>=2.9.0",
-    "pytest-raises>=0.11",
-    "pytest-runner>=5.2",
-    "pytest-runner>=5.2",
-    "pytest>=5.4.3",
-    "python-dotenv>=1.0.0",
-    "rtree",
-    "scikit-learn>=1.1.3",
-    "scikit-learn>=1.1.3",
-    "scipy>=1.6.2",
-    "seaborn>=0.12.1",
-    "seaborn>=0.12.1",
-    "simulariumio>=1.6.3",
     "sphinx_rtd_theme>=0.5.1",
     "tox>=3.15.2",
-    "tqdm>=4.64.1",
-    "tqdm>=4.64.1",
-    "trimesh>=3.9.34",
-    "twine>=3.1.1",
     "wheel>=0.34.2",
+    "tox-pdm>=0.7.2",
 ]
 
-[project.scripts]
-analyze = "cellpack.bin.analyze:main"
-convert = "cellpack.bin.simularium_converter:main"
-pack = "cellpack.bin.pack:main"
-upload = "cellpack.bin.upload:main"
+[tool.pdm.scripts]
+requirements = "pdm export -f requirements --without-hashes -o"
 
 [build-system]
 requires = ["pdm-backend"]
-build-backend = "pdm.backend"
+build-backend = "pdm.backend"
\ No newline at end of file