diff --git a/poetry.lock b/poetry.lock
index a72c839..35b6706 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand.
 
 [[package]]
 name = "appdirs"
@@ -6,6 +6,7 @@ version = "1.4.4"
 description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
     {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
@@ -17,6 +18,7 @@ version = "1.84"
 description = "Freely available tools for computational molecular biology."
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b"},
     {file = "biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4"},
@@ -54,6 +56,7 @@ version = "0.1.188"
 description = "Command-line program and library for reading, writing, validating and executing modeling projects (COMBINE/OMEX archives with SED-ML files)."
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "biosimulators_utils-0.1.188-py2.py3-none-any.whl", hash = "sha256:61ba2388b109ac3b8832f1a1244b633bef067a082c35d824eb6078217e01555a"},
     {file = "biosimulators_utils-0.1.188.tar.gz", hash = "sha256:ab64a0ec50ea3b073735a070701a119a9b5c1dd7c66d889afe9a9e179832af5b"},
@@ -110,6 +113,7 @@ version = "3.0"
 description = "Easily capture stdout/stderr of the current process and subprocesses"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
 files = [
     {file = "capturer-3.0-py2.py3-none-any.whl", hash = "sha256:b1ef6e8831cd170906df7c881a36c8b8a1b0b824b147b950a1a8c11776da981b"},
     {file = "capturer-3.0.tar.gz", hash = "sha256:4849032f6a670c02be434c484a0abf43c870a1efafafbfffd2e6f1c1f7ef5001"},
@@ -124,6 +128,7 @@ version = "3.0.10"
 description = "Application Framework for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "cement-3.0.10-py3-none-any.whl", hash = "sha256:8b70a26f0cfe53f1c90e972de27e2e78d180d13e386d11022dc8e65035b11f1e"},
     {file = "cement-3.0.10.tar.gz", hash = "sha256:73d1015ebf9b8df13e6bc987edf0d4be3f1c8b4438921eea8d66cbb5504aee15"},
@@ -146,6 +151,7 @@ version = "2024.7.4"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
     {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
@@ -157,6 +163,7 @@ version = "5.2.0"
 description = "Universal encoding detector for Python 3"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"},
     {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"},
@@ -168,6 +175,7 @@ version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
+groups = ["main"]
 files = [
     {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
     {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
@@ -267,6 +275,8 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["dev"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
@@ -278,6 +288,7 @@ version = "7.1.0"
 description = "Updated configparser from stdlib for earlier Pythons."
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "configparser-7.1.0-py3-none-any.whl", hash = "sha256:98e374573c4e10e92399651e3ba1c47a438526d633c44ee96143dec26dad4299"},
     {file = "configparser-7.1.0.tar.gz", hash = "sha256:eb82646c892dbdf773dae19c633044d163c3129971ae09b49410a303b8e0a5f7"},
@@ -285,7 +296,7 @@ files = [
 
 [package.extras]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "types-backports"]
+test = ["pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\"", "types-backports"]
 
 [[package]]
 name = "contourpy"
@@ -293,6 +304,7 @@ version = "1.2.1"
 description = "Python library for calculating contours of 2D quadrilateral grids"
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "contourpy-1.2.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bd7c23df857d488f418439686d3b10ae2fbf9bc256cd045b37a8c16575ea1040"},
     {file = "contourpy-1.2.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:5b9eb0ca724a241683c9685a484da9d35c872fd42756574a7cfbf58af26677fd"},
@@ -356,6 +368,7 @@ version = "0.12.1"
 description = "Composable style cycles"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -371,6 +384,7 @@ version = "1.1.0"
 description = "An implementation of lxml.xmlfile for the standard library"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "et_xmlfile-1.1.0-py3-none-any.whl", hash = "sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada"},
     {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"},
@@ -382,6 +396,7 @@ version = "2.0.3"
 description = "Validation and secure evaluation of untrusted python expressions"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "evalidate-2.0.3-py3-none-any.whl", hash = "sha256:0ec20b9b29649c7b93436e05254d1871e3137c6c91c13973436393d648a7461c"},
     {file = "evalidate-2.0.3.tar.gz", hash = "sha256:5a18e1bd7427ccde2518bad90d7bcec07308a2346822ac094e8fcf8094b8fab8"},
@@ -393,6 +408,8 @@ version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
     {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
@@ -407,6 +424,7 @@ version = "0.12.3"
 description = "Faultless AST for Open Biomedical Ontologies in Python."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "fastobo-0.12.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:79fe4f5ba1ec1a2bc1ca0d65834cfc622db639128ba89019328937e623c54094"},
     {file = "fastobo-0.12.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:21c347ec270d0ef6e120ba701370a8ef20953654b397d2814f62595d4d7c0062"},
@@ -462,6 +480,7 @@ version = "0.3"
 description = "Saves and loads to the cache a transformed versions of a source object."
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "flexcache-0.3-py3-none-any.whl", hash = "sha256:d43c9fea82336af6e0115e308d9d33a185390b8346a017564611f1466dcd2e32"},
     {file = "flexcache-0.3.tar.gz", hash = "sha256:18743bd5a0621bfe2cf8d519e4c3bfdf57a269c15d1ced3fb4b64e0ff4600656"},
@@ -479,6 +498,7 @@ version = "0.3.1"
 description = "Parsing made fun ... using typing."
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "flexparser-0.3.1-py3-none-any.whl", hash = "sha256:2e3e2936bec1f9277f777ef77297522087d96adb09624d4fe4240fd56885c013"},
     {file = "flexparser-0.3.1.tar.gz", hash = "sha256:36f795d82e50f5c9ae2fde1c33f21f88922fdd67b7629550a3cc4d0b40a66856"},
@@ -496,6 +516,7 @@ version = "4.53.1"
 description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "fonttools-4.53.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:0679a30b59d74b6242909945429dbddb08496935b82f91ea9bf6ad240ec23397"},
     {file = "fonttools-4.53.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e8bf06b94694251861ba7fdeea15c8ec0967f84c3d4143ae9daf42bbc7717fe3"},
@@ -542,18 +563,18 @@ files = [
 ]
 
 [package.extras]
-all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "pycairo", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
+all = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "fs (>=2.2.0,<3)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\"", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0) ; python_version <= \"3.12\"", "xattr ; sys_platform == \"darwin\"", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["munkres", "pycairo", "scipy"]
+interpolatable = ["munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\""]
 lxml = ["lxml (>=4.0)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
 repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
-type1 = ["xattr"]
+type1 = ["xattr ; sys_platform == \"darwin\""]
 ufo = ["fs (>=2.2.0,<3)"]
-unicode = ["unicodedata2 (>=15.1.0)"]
-woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
+unicode = ["unicodedata2 (>=15.1.0) ; python_version <= \"3.12\""]
+woff = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "glob2"
@@ -561,6 +582,7 @@ version = "0.7"
 description = "Version of the glob module that can capture patterns and supports recursive wildcards"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "glob2-0.7.tar.gz", hash = "sha256:85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c"},
 ]
@@ -571,6 +593,7 @@ version = "0.20.3"
 description = "Simple Python interface for Graphviz"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "graphviz-0.20.3-py3-none-any.whl", hash = "sha256:81f848f2904515d8cd359cc611faba817598d2feaac4027b266aa3eda7b3dde5"},
     {file = "graphviz-0.20.3.zip", hash = "sha256:09d6bc81e6a9fa392e7ba52135a9d49f1ed62526f96499325930e87ca1b5925d"},
@@ -587,6 +610,7 @@ version = "3.11.0"
 description = "Read and write HDF5 files from Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "h5py-3.11.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1625fd24ad6cfc9c1ccd44a66dac2396e7ee74940776792772819fc69f3a3731"},
     {file = "h5py-3.11.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c072655ad1d5fe9ef462445d3e77a8166cbfa5e599045f8aa3c19b75315f10e5"},
@@ -620,6 +644,7 @@ version = "10.0"
 description = "Human friendly output for text interfaces using Python"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main"]
 files = [
     {file = "humanfriendly-10.0-py2.py3-none-any.whl", hash = "sha256:1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477"},
     {file = "humanfriendly-10.0.tar.gz", hash = "sha256:6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc"},
@@ -634,6 +659,7 @@ version = "3.8"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "idna-3.8-py3-none-any.whl", hash = "sha256:050b4e5baadcd44d760cedbd2b8e639f2ff89bbc7a5730fcc662954303377aac"},
     {file = "idna-3.8.tar.gz", hash = "sha256:d838c2c0ed6fced7693d5e8ab8e734d5f8fda53a039c0164afb0b82e771e3603"},
@@ -645,6 +671,7 @@ version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
     {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
     {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
@@ -656,6 +683,7 @@ version = "0.6.1"
 description = "An ISO 8601 date/time/duration parser and formatter"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"},
     {file = "isodate-0.6.1.tar.gz", hash = "sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9"},
@@ -670,6 +698,7 @@ version = "2.34"
 description = "Utilities for working with the Kinetic Simulation Algorithm Ontology (KiSAO)"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "kisao-2.34-py2.py3-none-any.whl", hash = "sha256:f685f66e08935bf1a2d7dc0152a372b10e3661d0659f8e89329dcc716a723da2"},
     {file = "kisao-2.34.tar.gz", hash = "sha256:dd0a0e958131b2b577764d9060bec2aa2ceeef88534e5ec740054c4d20bc9395"},
@@ -689,6 +718,7 @@ version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "kiwisolver-1.4.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:05703cf211d585109fcd72207a31bb170a0f22144d68298dc5e61b3c946518af"},
     {file = "kiwisolver-1.4.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:146d14bebb7f1dc4d5fbf74f8a6cb15ac42baadee8912eb84ac0b3b2a3dc6ac3"},
@@ -802,6 +832,7 @@ version = "5.3.0"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "lxml-5.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:dd36439be765e2dde7660212b5275641edbc813e7b24668831a5c8ac91180656"},
     {file = "lxml-5.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ae5fe5c4b525aa82b8076c1a59d642c17b6e8739ecf852522c6321852178119d"},
@@ -956,6 +987,7 @@ version = "3.9.2"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "matplotlib-3.9.2-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:9d78bbc0cbc891ad55b4f39a48c22182e9bdaea7fc0e5dbd364f49f729ca1bbb"},
     {file = "matplotlib-3.9.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c375cc72229614632c87355366bdf2570c2dac01ac66b8ad048d2dabadf2d0d4"},
@@ -1019,6 +1051,7 @@ version = "1.3.0"
 description = "Python library for arbitrary-precision floating-point arithmetic"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "mpmath-1.3.0-py3-none-any.whl", hash = "sha256:a0b2b9fe80bbcd81a6647ff13108738cfb482d481d826cc0e02f5b35e5c88d2c"},
     {file = "mpmath-1.3.0.tar.gz", hash = "sha256:7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f"},
@@ -1027,7 +1060,7 @@ files = [
 [package.extras]
 develop = ["codecov", "pycodestyle", "pytest (>=4.6)", "pytest-cov", "wheel"]
 docs = ["sphinx"]
-gmpy = ["gmpy2 (>=2.1.0a4)"]
+gmpy = ["gmpy2 (>=2.1.0a4) ; platform_python_implementation != \"PyPy\""]
 tests = ["pytest (>=4.6)"]
 
 [[package]]
@@ -1036,6 +1069,7 @@ version = "8.4.0"
 description = "Simple yet flexible natural sorting in Python."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "natsort-8.4.0-py3-none-any.whl", hash = "sha256:4732914fb471f56b5cce04d7bae6f164a592c7712e1c85f9ef585e197299521c"},
     {file = "natsort-8.4.0.tar.gz", hash = "sha256:45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581"},
@@ -1051,6 +1085,7 @@ version = "3.3"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
 python-versions = ">=3.10"
+groups = ["main"]
 files = [
     {file = "networkx-3.3-py3-none-any.whl", hash = "sha256:28575580c6ebdaf4505b22c6256a2b9de86b316dc63ba9e93abde3d78dfdbcf2"},
     {file = "networkx-3.3.tar.gz", hash = "sha256:0c127d8b2f4865f59ae9cb8aafcd60b5c70f3241ebd66f7defad7c4ab90126c9"},
@@ -1069,6 +1104,7 @@ version = "2.1.0"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.10"
+groups = ["main"]
 files = [
     {file = "numpy-2.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6326ab99b52fafdcdeccf602d6286191a79fe2fda0ae90573c5814cd2b0bc1b8"},
     {file = "numpy-2.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0937e54c09f7a9a68da6889362ddd2ff584c02d015ec92672c099b61555f8911"},
@@ -1130,6 +1166,7 @@ version = "3.1.5"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "openpyxl-3.1.5-py2.py3-none-any.whl", hash = "sha256:5282c12b107bffeef825f4617dc029afaf41d0ea60823bbb665ef3079dc79de2"},
     {file = "openpyxl-3.1.5.tar.gz", hash = "sha256:cf0e3cf56142039133628b5acffe8ef0c12bc902d2aadd3e0fe5878dc08d1050"},
@@ -1144,6 +1181,7 @@ version = "24.1"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "dev"]
 files = [
     {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"},
     {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
@@ -1155,6 +1193,7 @@ version = "2.2.2"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "pandas-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:90c6fca2acf139569e74e8781709dccb6fe25940488755716d1d354d6bc58bce"},
     {file = "pandas-2.2.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c7adfc142dac335d8c1e0dcbd37eb8617eac386596eb9e1a1b77791cf2498238"},
@@ -1228,6 +1267,7 @@ version = "10.4.0"
 description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "pillow-10.4.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:4d9667937cfa347525b319ae34375c37b9ee6b525440f3ef48542fcf66f2731e"},
     {file = "pillow-10.4.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:543f3dc61c18dafb755773efc89aae60d06b6596a63914107f75459cf984164d"},
@@ -1316,7 +1356,7 @@ docs = ["furo", "olefile", "sphinx (>=7.3)", "sphinx-copybutton", "sphinx-inline
 fpx = ["olefile"]
 mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
-typing = ["typing-extensions"]
+typing = ["typing-extensions ; python_version < \"3.10\""]
 xmp = ["defusedxml"]
 
 [[package]]
@@ -1325,6 +1365,7 @@ version = "0.24.3"
 description = "Physical quantities module"
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "Pint-0.24.3-py3-none-any.whl", hash = "sha256:d98667e46fd03a1b94694fbfa104ec30858684d8ab26952e2a348b48059089bb"},
     {file = "pint-0.24.3.tar.gz", hash = "sha256:d54771093e8b94c4e0a35ac638c2444ddf3ef685652bab7675ffecfa0c5c5cdf"},
@@ -1354,6 +1395,7 @@ version = "24.2"
 description = "The PyPA recommended tool for installing Python packages."
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "pip-24.2-py3-none-any.whl", hash = "sha256:2cd581cf58ab7fcfca4ce8efa6dcacd0de5bf8d0a3eb9ec927e07405f4d9e2a2"},
     {file = "pip-24.2.tar.gz", hash = "sha256:5b5e490b5e9cb275c879595064adce9ebd31b854e3e803740b72f9ccf34a45b8"},
@@ -1365,6 +1407,7 @@ version = "0.0.5"
 description = "Utilities for linking setuptools with version metadata, README files, requirements files, and restoring overridden entry points"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "pkg_utils-0.0.5-py2.py3-none-any.whl", hash = "sha256:8bf375216e3dfac4e4d0666a23553e3240e89372c51396752c3bdf03b9fa924d"},
     {file = "pkg_utils-0.0.5.tar.gz", hash = "sha256:dd64e37e73dfb64cb153203c4e7a46d44a0a7b8fc563586210cce8f0042b59a3"},
@@ -1388,6 +1431,7 @@ version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
     {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
@@ -1403,6 +1447,7 @@ version = "2.5.7"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "pronto-2.5.7-py2.py3-none-any.whl", hash = "sha256:d7a053cb1735353ef1c708226e77d051a1a32906b5c77f89f9d99c6ca5b5c985"},
     {file = "pronto-2.5.7.tar.gz", hash = "sha256:014a5b02064781d6edd7ca5b4f63b13342dd9b5322248f5a4740f48a98464629"},
@@ -1420,6 +1465,7 @@ version = "3.0.1"
 description = "Python interface to Graphviz's Dot"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "pydot-3.0.1-py3-none-any.whl", hash = "sha256:43f1e878dc1ff7c1c2e3470a6999d4e9e97771c5c862440c2f0af0ba844c231f"},
     {file = "pydot-3.0.1.tar.gz", hash = "sha256:e18cf7f287c497d77b536a3d20a46284568fea390776dface6eabbdf1b1b5efc"},
@@ -1439,6 +1485,7 @@ version = "1.2.14"
 description = ""
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "pyomexmeta-1.2.14-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:5394ea8f89b9e4bfdd0bc7c6173537d6858645fe04763618288d8ed855f03c2c"},
     {file = "pyomexmeta-1.2.14-cp310-cp310-macosx_13_0_arm64.whl", hash = "sha256:000e0b7dfad84d6c570139a231ae76cec2d770a600e39d6df7376f0a7c567d5f"},
@@ -1469,6 +1516,7 @@ version = "3.1.4"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
+groups = ["main"]
 files = [
     {file = "pyparsing-3.1.4-py3-none-any.whl", hash = "sha256:a6a7ee4235a3f944aa1fa2249307708f893fe5717dc603503c6c7969c070fb7c"},
     {file = "pyparsing-3.1.4.tar.gz", hash = "sha256:f86ec8d1a83f11977c9a6ea7598e8c27fc5cddfa5b07ea2241edbbde1d7bc032"},
@@ -1483,6 +1531,8 @@ version = "3.4.1"
 description = "A python implementation of GNU readline."
 optional = false
 python-versions = "*"
+groups = ["main"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "pyreadline3-3.4.1-py3-none-any.whl", hash = "sha256:b0efb6516fd4fb07b45949053826a62fa4cb353db5be2bbb4a7aa1fdd1e345fb"},
     {file = "pyreadline3-3.4.1.tar.gz", hash = "sha256:6f3d1f7b8a31ba32b73917cefc1f28cc660562f39aea8646d30bd6eff21f7bae"},
@@ -1494,6 +1544,7 @@ version = "8.3.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pytest-8.3.2-py3-none-any.whl", hash = "sha256:4ba08f9ae7dcf84ded419494d229b48d0903ea6407b030eaec46df5e6a73bba5"},
     {file = "pytest-8.3.2.tar.gz", hash = "sha256:c132345d12ce551242c87269de812483f5bcc87cdbb4722e48487ba194f9fdce"},
@@ -1516,6 +1567,7 @@ version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+groups = ["main"]
 files = [
     {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
     {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
@@ -1530,6 +1582,7 @@ version = "0.2.20"
 description = "LibCombine Python API"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "python-libcombine-0.2.20.tar.gz", hash = "sha256:d41bc1df3df6c0bf04a99680b78b213a47063564e0e15d4f998cfaa37550b579"},
     {file = "python_libcombine-0.2.20-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:faaf0b5674a4d52150318f77bbfe22c7a33ad9540a31d6f2bc7b264584dbc7a3"},
@@ -1556,6 +1609,14 @@ files = [
     {file = "python_libcombine-0.2.20-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:bdd3eea14ad35b854132c09218ff76119547ccbebc22c2200495104e2bbf7972"},
     {file = "python_libcombine-0.2.20-cp312-cp312-win32.whl", hash = "sha256:64e2c3aa1e055464583265578a721ade8771dafd858069ea8cd9d762918fda79"},
     {file = "python_libcombine-0.2.20-cp312-cp312-win_amd64.whl", hash = "sha256:ef03f7f7ddb1a6025fcf09eb848950c8b599e046a345faf7e2abf9600f2246d6"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:697c48f4ec1500e0b7d45a5fd1a86199c4c78a9180ec2b019f0586b820c0e892"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:66f9ab188c2bda1939b9bd43f6fd130025401638f4dfcd221a2604d9b05c98a0"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7b9ac876b3610e1e3d1b0ea8d2a620bb6b5ec73b70056ff750fb7983ec62b631"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3c34c09579d78c84593b45b504fc80d43943c864e5933e77fc519a8603f657c6"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:2f721f2342df34cae9a469b61b8a001178164b8042dc6259ee4cf611b4a0eb7a"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:5f750f9c97fe01a8e4bff7e67995dfc5352b43836e11368abadee3cbc8770e14"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-win32.whl", hash = "sha256:4d9a060e43e6e19643a381a6b3e2be5a4f577677cdc695eae6558212b4d0ffe0"},
+    {file = "python_libcombine-0.2.20-cp313-cp313-win_amd64.whl", hash = "sha256:aa40bab49d97a9dcfb3c4d928b73a1f7b6a839a9c280ac644cb506a8d062713a"},
     {file = "python_libcombine-0.2.20-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:78793c7c34138fcc091e0fce41ae80a29bf03ed9574c6f0ecec28eb49ba6ae5f"},
     {file = "python_libcombine-0.2.20-cp37-cp37m-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:52ba93087f3fa5478ee2be7cdeaa885334d56e6092ba21061e5606e59cd02712"},
     {file = "python_libcombine-0.2.20-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a281dc3cd6fbcdcab73c1a670bda94f5b0b9cd9186d6db1968212c8e9191e9b2"},
@@ -1587,6 +1648,7 @@ version = "2.0.32"
 description = "LibSedML Python API"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "python_libsedml-2.0.32-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7d3e0dd299eea0d2e6925a5e55354e0ff45890195925a7c0a1bcd65f2c93c722"},
     {file = "python_libsedml-2.0.32-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:47e7e76e836c6e4b55b080e0fa6f9df2645abfcf79fe089f9b4339f703501304"},
@@ -1614,6 +1676,14 @@ files = [
     {file = "python_libsedml-2.0.32-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:b2fe8c0cc6f8beec72733bf987de9fe7880ca638036f64538c4cc3ece78b7c3d"},
     {file = "python_libsedml-2.0.32-cp312-cp312-win32.whl", hash = "sha256:3195bad01e02316bad1f5a82e83a9467f24555575fffc180861fb65b6f41f50e"},
     {file = "python_libsedml-2.0.32-cp312-cp312-win_amd64.whl", hash = "sha256:25df3d7954e946ba1fdc868982848a15d84dd0e30ff8ed4ad0f8a617b9639cda"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:38bacb3bdac5c136b27ec44af6de52f418639fc7a1d52d755d4b8a23689fbb1a"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:e39f8fe3c5e055e23d6876f37464249f0c9dd69a673543dfe2697a9ea4f4d718"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:46521927cfcc4d0ae0a4b439faee0ea64bee4551d2c587ddd808efab35a1853d"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1b3982394b93d8581c08731cd4d9734a3a5df3ef54ff7a53fcb35bbd93dcb850"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:f3353ded3fb38b9f7c291383ade9e7537482ca44b9abd61fdb3fcb3f2b489dca"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:fe7956e9c50c3cb40676d0bd413eb00d2274635b41842b2dfce19b6e08ea8159"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-win32.whl", hash = "sha256:24783f6fc5ec3516ed072eadfaa61984c2d8e73b9ca5e6af0328456a66690fda"},
+    {file = "python_libsedml-2.0.32-cp313-cp313-win_amd64.whl", hash = "sha256:9784868734e624850f07efde441ac7d1f4c6ff2ad78d2e1865e8595617c4e0c0"},
     {file = "python_libsedml-2.0.32-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3b2a7321de6906d9e26f58c708c1dddeeaed67e61a080f856aaa19847455040b"},
     {file = "python_libsedml-2.0.32-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:a822c7df4141a4c5e7e9c3487f9d0b2ec39c62b7cc18e7ed2ccd7bc2b543e6ff"},
     {file = "python_libsedml-2.0.32-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b7334678f5a236ed9b4ab6d5f71144d82a3e6aef283455486c82c820e32e7f9f"},
@@ -1652,6 +1722,7 @@ version = "2024.1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
     {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
@@ -1663,6 +1734,8 @@ version = "306"
 description = "Python for Window Extensions"
 optional = false
 python-versions = "*"
+groups = ["main"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "pywin32-306-cp310-cp310-win32.whl", hash = "sha256:06d3420a5155ba65f0b72f2699b5bacf3109f36acbe8923765c22938a69dfc8d"},
     {file = "pywin32-306-cp310-cp310-win_amd64.whl", hash = "sha256:84f4471dbca1887ea3803d8848a1616429ac94a4a8d05f4bc9c5dcfd42ca99c8"},
@@ -1686,6 +1759,7 @@ version = "6.0.2"
 description = "YAML parser and emitter for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"},
     {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"},
@@ -1748,6 +1822,7 @@ version = "6.2.0"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "rdflib-6.2.0-py3-none-any.whl", hash = "sha256:85c34a86dfc517a41e5f2425a41a0aceacc23983462b32e68610b9fad1383bca"},
     {file = "rdflib-6.2.0.tar.gz", hash = "sha256:62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942"},
@@ -1760,7 +1835,7 @@ setuptools = "*"
 
 [package.extras]
 berkeleydb = ["berkeleydb"]
-dev = ["black (==22.6.0)", "flake8", "flakeheaven", "isort", "mypy", "pep8-naming", "types-setuptools"]
+dev = ["black (==22.6.0)", "flake8", "flakeheaven ; python_version >= \"3.8.0\"", "isort", "mypy", "pep8-naming", "types-setuptools"]
 docs = ["myst-parser", "sphinx (<6)", "sphinx-autodoc-typehints", "sphinxcontrib-apidoc", "sphinxcontrib-kroki"]
 html = ["html5lib"]
 networkx = ["networkx"]
@@ -1772,6 +1847,7 @@ version = "2024.7.24"
 description = "Alternative regular expression module, to replace re."
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "regex-2024.7.24-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:228b0d3f567fafa0633aee87f08b9276c7062da9616931382993c03808bb68ce"},
     {file = "regex-2024.7.24-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:3426de3b91d1bc73249042742f45c2148803c111d1175b283270177fdf669024"},
@@ -1860,6 +1936,7 @@ version = "2.32.3"
 description = "Python HTTP for Humans."
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"},
     {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"},
@@ -1881,6 +1958,7 @@ version = "0.2.0"
 description = "Parses Pip requirement files"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "requirements-parser-0.2.0.tar.gz", hash = "sha256:5963ee895c2d05ae9f58d3fc641082fb38021618979d6a152b6b1398bd7d4ed4"},
     {file = "requirements_parser-0.2.0-py2-none-any.whl", hash = "sha256:76650b4a9d98fc65edf008a7920c076bb2a76c08eaae230ce4cfc6f51ea6a773"},
@@ -1892,15 +1970,16 @@ version = "73.0.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "setuptools-73.0.1-py3-none-any.whl", hash = "sha256:b208925fcb9f7af924ed2dc04708ea89791e24bde0d3020b27df0e116088b34e"},
     {file = "setuptools-73.0.1.tar.gz", hash = "sha256:d59a3e788ab7e012ab2c4baed1b376da6366883ee20d7a5fc426816e3d7b1193"},
 ]
 
 [package.extras]
-core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+core = ["importlib-metadata (>=6) ; python_version < \"3.10\"", "importlib-resources (>=5.10.2) ; python_version < \"3.9\"", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1) ; python_version < \"3.11\"", "wheel (>=0.43.0)"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
-test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21) ; python_version >= \"3.9\" and sys_platform != \"cygwin\"", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf ; sys_platform != \"cygwin\"", "pytest-ruff (<0.4) ; platform_system == \"Windows\"", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\"", "pytest-ruff (>=0.3.2) ; sys_platform != \"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
 
 [[package]]
 name = "simplejson"
@@ -1908,6 +1987,7 @@ version = "3.19.3"
 description = "Simple, fast, extensible JSON encoder/decoder for Python"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.5"
+groups = ["main"]
 files = [
     {file = "simplejson-3.19.3-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:f39caec26007a2d0efab6b8b1d74873ede9351962707afab622cc2285dd26ed0"},
     {file = "simplejson-3.19.3-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:83c87706265ae3028e8460d08b05f30254c569772e859e5ba61fe8af2c883468"},
@@ -2027,6 +2107,7 @@ version = "1.11.0"
 description = "Python package that converts simulation outputs to the format consumed by the Simularium viewer website"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "simulariumio-1.11.0-py3-none-any.whl", hash = "sha256:a23026e8ad650d88478094cfa293562320844ba87246562a5e2a8325e1718ee4"},
     {file = "simulariumio-1.11.0.tar.gz", hash = "sha256:4f58c25ec633a4f260e78e4ed5c1d89fa12468cf3f3ee2061fe039c83f23c894"},
@@ -2055,6 +2136,7 @@ version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+groups = ["main"]
 files = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -2066,6 +2148,7 @@ version = "2.73"
 description = "Python package for the Smoldyn simulator"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
     {file = "smoldyn-2.73-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:071c5370390de1227197e5ae11b36bdfdd52e6595d9937a1a7b98e749aa69978"},
     {file = "smoldyn-2.73-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:28f5ecf0f6c7b615c6dde85fa3a4a9c6798fe0bdbfcfd3f58b8c1eb7294425dc"},
@@ -2096,6 +2179,7 @@ version = "2.4.0"
 description = "ANSI color formatting for output in terminal"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "termcolor-2.4.0-py3-none-any.whl", hash = "sha256:9297c0df9c99445c2412e832e882a7884038a25617c60cea2ad69488d4040d63"},
     {file = "termcolor-2.4.0.tar.gz", hash = "sha256:aab9e56047c8ac41ed798fa36d892a37aca6b3e9159f3e0c24bc64a9b3ac7b7a"},
@@ -2110,6 +2194,7 @@ version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+groups = ["dev"]
 files = [
     {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
     {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
@@ -2121,6 +2206,8 @@ version = "2.0.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
+markers = "python_version < \"3.11\""
 files = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
@@ -2132,6 +2219,7 @@ version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
     {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
@@ -2143,6 +2231,7 @@ version = "2024.1"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
+groups = ["main"]
 files = [
     {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
     {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
@@ -2154,6 +2243,7 @@ version = "4.0.3"
 description = "URI parsing, classification and composition"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "uritools-4.0.3-py3-none-any.whl", hash = "sha256:bae297d090e69a0451130ffba6f2f1c9477244aa0a5543d66aed2d9f77d0dd9c"},
     {file = "uritools-4.0.3.tar.gz", hash = "sha256:ee06a182a9c849464ce9d5fa917539aacc8edd2a4924d1b7aabeeecabcae3bc2"},
@@ -2161,17 +2251,18 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "2.2.2"
+version = "2.5.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
+groups = ["main"]
 files = [
-    {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"},
-    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
+    {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
+    {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
 h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
@@ -2182,6 +2273,7 @@ version = "0.1.8"
 description = "Python library for loading and dumping \"yamldown\" (markdown with embedded yaml) files."
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "yamldown-0.1.8-py3-none-any.whl", hash = "sha256:936ad7bdbde725d0bd3adb77236aae4eb75388619f31232595f7dd45f7006598"},
     {file = "yamldown-0.1.8.tar.gz", hash = "sha256:ec1056e5ec3c47a7c14f69d343b73256ad12751361f1a833805a8ee722cf883c"},
@@ -2191,6 +2283,6 @@ files = [
 pyYaml = "*"
 
 [metadata]
-lock-version = "2.0"
+lock-version = "2.1"
 python-versions = ">=3.10"
 content-hash = "5b5485aa9909339f96225183636a3dac9cb0b56d545ab0f14692fefeabd72d9a"