diff --git a/poetry.lock b/poetry.lock
index f0a3f683..eaf06820 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 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 = "accessible-pygments"
@@ -6,6 +6,7 @@ version = "0.0.5"
 description = "A collection of accessible pygments styles"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 files = [
     {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"},
     {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"},
@@ -24,6 +25,7 @@ version = "0.6.0"
 description = "Airspeed is a powerful and easy-to-use templating engine for Python that aims for a high level of compatibility with the popular Velocity library for Java."
 optional = false
 python-versions = "*"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "airspeed-0.6.0.tar.gz", hash = "sha256:3d795fbed445dd981aed27b9b38383cc7ff451eea19d7e02ec5141753c293f06"},
 ]
@@ -38,6 +40,7 @@ version = "1.0.0"
 description = "A light, configurable Sphinx theme"
 optional = false
 python-versions = ">=3.10"
+groups = ["docs"]
 files = [
     {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"},
     {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"},
@@ -49,6 +52,7 @@ version = "4.6.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "bngl"]
 files = [
     {file = "anyio-4.6.0-py3-none-any.whl", hash = "sha256:c7d2e9d63e31599eeb636c8c5c03a7e108d73b345f064f1c19fdc87b79036a9a"},
     {file = "anyio-4.6.0.tar.gz", hash = "sha256:137b4559cbb034c477165047febb6ff83f390fc3b20bf181c1fc0a728cb8beeb"},
@@ -62,7 +66,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.21.0b1)"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.21.0b1) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\""]
 trio = ["trio (>=0.26.1)"]
 
 [[package]]
@@ -71,6 +75,7 @@ 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", "lems", "simularium"]
 files = [
     {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
     {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
@@ -82,6 +87,8 @@ version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl"]
+markers = "platform_system == \"Darwin\""
 files = [
     {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
     {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
@@ -93,6 +100,7 @@ version = "23.1.0"
 description = "Argon2 for Python"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"},
     {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"},
@@ -113,6 +121,7 @@ version = "21.2.0"
 description = "Low-level CFFI bindings for Argon2"
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl"]
 files = [
     {file = "argon2-cffi-bindings-21.2.0.tar.gz", hash = "sha256:bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3"},
     {file = "argon2_cffi_bindings-21.2.0-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:ccb949252cb2ab3a08c02024acb77cfb179492d5701c7cbdbfd776124d4d2367"},
@@ -150,6 +159,7 @@ version = "1.3.0"
 description = "Better dates & times for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
     {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
@@ -169,6 +179,7 @@ version = "2.4.1"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
     {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
@@ -178,8 +189,8 @@ files = [
 six = ">=1.12.0"
 
 [package.extras]
-astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
-test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+astroid = ["astroid (>=1,<2) ; python_version < \"3\"", "astroid (>=2,<4) ; python_version >= \"3\""]
+test = ["astroid (>=1,<2) ; python_version < \"3\"", "astroid (>=2,<4) ; python_version >= \"3\"", "pytest"]
 
 [[package]]
 name = "async-lru"
@@ -187,6 +198,7 @@ version = "2.0.4"
 description = "Simple LRU cache for asyncio"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "async-lru-2.0.4.tar.gz", hash = "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627"},
     {file = "async_lru-2.0.4-py3-none-any.whl", hash = "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224"},
@@ -201,18 +213,19 @@ version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl", "dev", "lems", "neuroml"]
 files = [
     {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
     {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
 [package.extras]
-benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"]
+cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"]
+dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"]
 docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
-tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
+tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\"", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.9\" and python_version < \"3.13\""]
 
 [[package]]
 name = "babel"
@@ -220,6 +233,7 @@ version = "2.16.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "docs"]
 files = [
     {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
     {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
@@ -234,6 +248,7 @@ version = "4.12.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.6.0"
+groups = ["main", "bngl", "docs"]
 files = [
     {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"},
     {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
@@ -255,6 +270,7 @@ version = "2023.7.28"
 description = "Helper for Bézier Curves, Triangles, and Higher Order Objects"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "dev", "escher"]
 files = [
     {file = "bezier-2023.7.28-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5846838f53b1f63fc53a2fb6273966eeaf0e8d6ed81a25368bfda8cc4bfb1f0c"},
     {file = "bezier-2023.7.28-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:412b15c606183a0aaf9cbc40d4e1069638e60d6a8a80460fb3bd7fb69f92a6b8"},
@@ -291,6 +307,7 @@ version = "0.8.4"
 description = "A simple CLI and library for the BioNetGen modeling language"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "bionetgen-0.8.4-py3-none-any.whl", hash = "sha256:8d632350d7e8295518ed9463d0834e5ca542c424b43a3fc9d05da9b45ba9bebc"},
     {file = "bionetgen-0.8.4.tar.gz", hash = "sha256:8ed967ac13c364565500f05cab56860f2734a2ba1dd19fcac756c1691b16973f"},
@@ -318,6 +335,7 @@ 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"},
@@ -355,6 +373,7 @@ version = "6.1.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "bleach-6.1.0-py3-none-any.whl", hash = "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6"},
     {file = "bleach-6.1.0.tar.gz", hash = "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe"},
@@ -373,6 +392,7 @@ version = "2.7.1"
 description = "Python wrapper for the C-Blosc2 library"
 optional = false
 python-versions = "<4,>=3.10"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "blosc2-2.7.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ad698c6fca8dee677b7a1881206f7ac43ffd7c458733716a3de1e1f3c6ba1f79"},
     {file = "blosc2-2.7.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:5923a22fb7cfdad571b316930e8812618ba8b2ac1f37ac05edcf3eda71beed9f"},
@@ -411,6 +431,7 @@ version = "5.5.0"
 description = "Extensible memoizing collections and decorators"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292"},
     {file = "cachetools-5.5.0.tar.gz", hash = "sha256:2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a"},
@@ -422,6 +443,7 @@ 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", "dev", "logging"]
 files = [
     {file = "capturer-3.0-py2.py3-none-any.whl", hash = "sha256:b1ef6e8831cd170906df7c881a36c8b8a1b0b824b147b950a1a8c11776da981b"},
     {file = "capturer-3.0.tar.gz", hash = "sha256:4849032f6a670c02be434c484a0abf43c870a1efafafbfffd2e6f1c1f7ef5001"},
@@ -436,6 +458,7 @@ version = "24.1.2"
 description = "Composable complex class support for attrs and dataclasses."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "cattrs-24.1.2-py3-none-any.whl", hash = "sha256:67c7495b760168d931a10233f979b28dc04daf853b30752246f4f8471c6d68d0"},
     {file = "cattrs-24.1.2.tar.gz", hash = "sha256:8028cfe1ff5382df59dd36474a86e02d817b06eaf8af84555441bac915d2ef85"},
@@ -450,8 +473,8 @@ typing-extensions = {version = ">=4.1.0,<4.6.3 || >4.6.3", markers = "python_ver
 bson = ["pymongo (>=4.4.0)"]
 cbor2 = ["cbor2 (>=5.4.6)"]
 msgpack = ["msgpack (>=1.0.5)"]
-msgspec = ["msgspec (>=0.18.5)"]
-orjson = ["orjson (>=3.9.2)"]
+msgspec = ["msgspec (>=0.18.5) ; implementation_name == \"cpython\""]
+orjson = ["orjson (>=3.9.2) ; implementation_name == \"cpython\""]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
 ujson = ["ujson (>=5.7.0)"]
@@ -462,6 +485,7 @@ version = "3.0.10"
 description = "Application Framework for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "cement-3.0.10-py3-none-any.whl", hash = "sha256:8b70a26f0cfe53f1c90e972de27e2e78d180d13e386d11022dc8e65035b11f1e"},
     {file = "cement-3.0.10.tar.gz", hash = "sha256:73d1015ebf9b8df13e6bc987edf0d4be3f1c8b4438921eea8d66cbb5504aee15"},
@@ -484,6 +508,7 @@ version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl", "containers", "dev", "docs"]
 files = [
     {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
     {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
@@ -495,6 +520,7 @@ version = "1.17.1"
 description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "cffi-1.17.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:df8b1c11f177bc2313ec4b2d46baec87a5f3e71fc8b45dab2ee7cae86d9aba14"},
     {file = "cffi-1.17.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8f2cdc858323644ab277e9bb925ad72ae0e67f69e804f4898c070998d50b1a67"},
@@ -574,6 +600,7 @@ 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"},
@@ -585,6 +612,7 @@ 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", "bngl", "containers", "dev", "docs"]
 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"},
@@ -684,6 +712,8 @@ 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 = ["main", "bngl", "dev", "docs"]
+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"},
@@ -695,6 +725,7 @@ version = "6.8.2"
 description = "Add colours to the output of Python's logging module."
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl"]
 files = [
     {file = "colorlog-6.8.2-py3-none-any.whl", hash = "sha256:4dcbb62368e2800cb3c5abd348da7e53f6c362dda502ec27c560b2e58a66bd33"},
     {file = "colorlog-6.8.2.tar.gz", hash = "sha256:3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44"},
@@ -712,6 +743,7 @@ version = "0.2.2"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "comm-0.2.2-py3-none-any.whl", hash = "sha256:e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3"},
     {file = "comm-0.2.2.tar.gz", hash = "sha256:3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e"},
@@ -729,6 +761,7 @@ version = "1.3.0"
 description = "Python library for calculating contours of 2D quadrilateral grids"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "bngl", "lems", "neuroml"]
 files = [
     {file = "contourpy-1.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:880ea32e5c774634f9fcd46504bf9f080a41ad855f4fef54f5380f5133d343c7"},
     {file = "contourpy-1.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:76c905ef940a4474a6289c71d53122a4f77766eef23c03cd57016ce19d0f7b42"},
@@ -813,6 +846,7 @@ version = "7.6.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "coverage-7.6.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b06079abebbc0e89e6163b8e8f0e16270124c154dc6e4a47b413dd538859af16"},
     {file = "coverage-7.6.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:cf4b19715bccd7ee27b6b120e7e9dd56037b9c0681dcc1adc9ba9db3d417fa36"},
@@ -892,7 +926,7 @@ files = [
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
-toml = ["tomli"]
+toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
 
 [[package]]
 name = "cycler"
@@ -900,6 +934,7 @@ version = "0.12.1"
 description = "Composable style cycles"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "lems", "neuroml"]
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -915,6 +950,7 @@ version = "1.8.6"
 description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "debugpy-1.8.6-cp310-cp310-macosx_14_0_x86_64.whl", hash = "sha256:30f467c5345d9dfdcc0afdb10e018e47f092e383447500f125b4e013236bf14b"},
     {file = "debugpy-1.8.6-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5d73d8c52614432f4215d0fe79a7e595d0dd162b5c15233762565be2f014803b"},
@@ -946,6 +982,7 @@ version = "5.1.1"
 description = "Decorators for Humans"
 optional = false
 python-versions = ">=3.5"
+groups = ["main", "bngl"]
 files = [
     {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
     {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
@@ -957,6 +994,7 @@ version = "0.7.1"
 description = "XML bomb protection for Python stdlib modules"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main", "bngl"]
 files = [
     {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"},
     {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"},
@@ -968,6 +1006,7 @@ version = "0.3.9"
 description = "serialize all of Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "dill-0.3.9-py3-none-any.whl", hash = "sha256:468dff3b89520b474c0397703366b7b95eebe6303f108adf9b19da1f702be87a"},
     {file = "dill-0.3.9.tar.gz", hash = "sha256:81aa267dddf68cbfe8029c42ca9ec6a4ab3b22371d1c450abc54422577b4512c"},
@@ -983,6 +1022,7 @@ version = "2.7.0"
 description = "DNS toolkit"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "dnspython-2.7.0-py3-none-any.whl", hash = "sha256:b4c34b7d10b51bcc3a5071e7b8dee77939f1e878477eeecc965e9835f63c6c86"},
     {file = "dnspython-2.7.0.tar.gz", hash = "sha256:ce9c432eda0dc91cf618a5cedf1a4e142651196bbcd2c80e89ed5a907e5cfaf1"},
@@ -1003,6 +1043,7 @@ version = "7.1.0"
 description = "A Python library for the Docker Engine API."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "containers", "dev"]
 files = [
     {file = "docker-7.1.0-py3-none-any.whl", hash = "sha256:c96b93b7f0a746f9e77d325bcfb87422a3d8bd4f03136ae8a85b37f1898d5fc0"},
     {file = "docker-7.1.0.tar.gz", hash = "sha256:ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c"},
@@ -1025,6 +1066,7 @@ version = "0.16"
 description = "Parse Python docstrings in reST, Google and Numpydoc format"
 optional = false
 python-versions = ">=3.6,<4.0"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "docstring_parser-0.16-py3-none-any.whl", hash = "sha256:bf0a1387354d3691d102edef7ec124f219ef639982d096e26e3b60aeffa90637"},
     {file = "docstring_parser-0.16.tar.gz", hash = "sha256:538beabd0af1e2db0146b6bd3caa526c35a34d61af9fd2887f3a8a27a739aa6e"},
@@ -1036,6 +1078,7 @@ version = "0.21.2"
 description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 files = [
     {file = "docutils-0.21.2-py3-none-any.whl", hash = "sha256:dafca5b9e384f0e419294eb4d2ff9fa826435bf15f15b7bd45723e8ad76811b2"},
     {file = "docutils-0.21.2.tar.gz", hash = "sha256:3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f"},
@@ -1047,6 +1090,7 @@ 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"},
@@ -1058,6 +1102,7 @@ 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"},
@@ -1069,6 +1114,8 @@ version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl", "dev", "lems", "neuroml"]
+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"},
@@ -1083,13 +1130,14 @@ version = "2.1.0"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "executing-2.1.0-py2.py3-none-any.whl", hash = "sha256:8d63781349375b5ebccc3142f4b30350c0cd9c79f921cde38be2be4637e98eaf"},
     {file = "executing-2.1.0.tar.gz", hash = "sha256:8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab"},
 ]
 
 [package.extras]
-tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""]
 
 [[package]]
 name = "fastjsonschema"
@@ -1097,6 +1145,7 @@ version = "2.20.0"
 description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "fastjsonschema-2.20.0-py3-none-any.whl", hash = "sha256:5875f0b0fa7a0043a91e93a9b8f793bcbbba9691e7fd83dca95c28ba26d21f0a"},
     {file = "fastjsonschema-2.20.0.tar.gz", hash = "sha256:3d48fc5300ee96f5d116f10fe6f28d938e6008f59a6a025c2649475b87f76a23"},
@@ -1111,6 +1160,7 @@ 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"},
@@ -1166,6 +1216,7 @@ version = "7.1.1"
 description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
 python-versions = ">=3.8.1"
+groups = ["dev"]
 files = [
     {file = "flake8-7.1.1-py2.py3-none-any.whl", hash = "sha256:597477df7860daa5aa0fdd84bf5208a043ab96b8e96ab708770ae0364dd03213"},
     {file = "flake8-7.1.1.tar.gz", hash = "sha256:049d058491e228e03e67b390f311bbf88fce2dbaa8fa673e7aea87b7198b8d38"},
@@ -1182,6 +1233,7 @@ version = "3.8.1"
 description = "Plugin for pytest that automatically reruns flaky tests."
 optional = false
 python-versions = ">=3.5"
+groups = ["dev"]
 files = [
     {file = "flaky-3.8.1-py2.py3-none-any.whl", hash = "sha256:194ccf4f0d3a22b2de7130f4b62e45e977ac1b5ccad74d4d48f3005dcc38815e"},
     {file = "flaky-3.8.1.tar.gz", hash = "sha256:47204a81ec905f3d5acfbd61daeabcada8f9d4031616d9bcb0618461729699f5"},
@@ -1193,6 +1245,7 @@ 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", "lems", "simularium"]
 files = [
     {file = "flexcache-0.3-py3-none-any.whl", hash = "sha256:d43c9fea82336af6e0115e308d9d33a185390b8346a017564611f1466dcd2e32"},
     {file = "flexcache-0.3.tar.gz", hash = "sha256:18743bd5a0621bfe2cf8d519e4c3bfdf57a269c15d1ced3fb4b64e0ff4600656"},
@@ -1210,6 +1263,7 @@ version = "0.3.1"
 description = "Parsing made fun ... using typing."
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "lems", "simularium"]
 files = [
     {file = "flexparser-0.3.1-py3-none-any.whl", hash = "sha256:2e3e2936bec1f9277f777ef77297522087d96adb09624d4fe4240fd56885c013"},
     {file = "flexparser-0.3.1.tar.gz", hash = "sha256:36f795d82e50f5c9ae2fde1c33f21f88922fdd67b7629550a3cc4d0b40a66856"},
@@ -1227,6 +1281,7 @@ version = "4.54.1"
 description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "lems", "neuroml"]
 files = [
     {file = "fonttools-4.54.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7ed7ee041ff7b34cc62f07545e55e1468808691dddfd315d51dd82a6b37ddef2"},
     {file = "fonttools-4.54.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:41bb0b250c8132b2fcac148e2e9198e62ff06f3cc472065dff839327945c5882"},
@@ -1279,18 +1334,18 @@ 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 = "fqdn"
@@ -1298,6 +1353,7 @@ version = "1.5.1"
 description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
 optional = false
 python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
+groups = ["main", "bngl"]
 files = [
     {file = "fqdn-1.5.1-py3-none-any.whl", hash = "sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014"},
     {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"},
@@ -1309,6 +1365,7 @@ version = "0.20.3"
 description = "Simple Python interface for Graphviz"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "graphviz-0.20.3-py3-none-any.whl", hash = "sha256:81f848f2904515d8cd359cc611faba817598d2feaac4027b266aa3eda7b3dde5"},
     {file = "graphviz-0.20.3.zip", hash = "sha256:09d6bc81e6a9fa392e7ba52135a9d49f1ed62526f96499325930e87ca1b5925d"},
@@ -1325,6 +1382,7 @@ version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "h11-0.14.0-py3-none-any.whl", hash = "sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761"},
     {file = "h11-0.14.0.tar.gz", hash = "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d"},
@@ -1336,6 +1394,7 @@ version = "3.12.1"
 description = "Read and write HDF5 files from Python"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "h5py-3.12.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2f0f1a382cbf494679c07b4371f90c70391dedb027d517ac94fa2c05299dacda"},
     {file = "h5py-3.12.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:cb65f619dfbdd15e662423e8d257780f9a66677eae5b4b3fc9dca70b5fd2d2a3"},
@@ -1374,6 +1433,7 @@ version = "1.0.6"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "httpcore-1.0.6-py3-none-any.whl", hash = "sha256:27b59625743b85577a8c0e10e55b50b5368a4f2cfe8cc7bcfa9cf00829c2682f"},
     {file = "httpcore-1.0.6.tar.gz", hash = "sha256:73f6dbd6eb8c21bbf7ef8efad555481853f5f6acdeaff1edb0694289269ee17f"},
@@ -1395,6 +1455,7 @@ version = "0.27.2"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "httpx-0.27.2-py3-none-any.whl", hash = "sha256:7bb2708e112d8fdd7829cd4243970f0c223274051cb35ee80c03301ee29a3df0"},
     {file = "httpx-0.27.2.tar.gz", hash = "sha256:f7c2be1d2f3c3c3160d441802406b206c2b76f5947b11115e6df10c6c65e66c2"},
@@ -1408,7 +1469,7 @@ idna = "*"
 sniffio = "*"
 
 [package.extras]
-brotli = ["brotli", "brotlicffi"]
+brotli = ["brotli ; platform_python_implementation == \"CPython\"", "brotlicffi ; platform_python_implementation != \"CPython\""]
 cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
@@ -1420,6 +1481,7 @@ 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", "dev", "logging"]
 files = [
     {file = "humanfriendly-10.0-py2.py3-none-any.whl", hash = "sha256:1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477"},
     {file = "humanfriendly-10.0.tar.gz", hash = "sha256:6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc"},
@@ -1434,6 +1496,7 @@ version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl", "containers", "dev", "docs"]
 files = [
     {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
     {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
@@ -1448,6 +1511,7 @@ version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["docs"]
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -1459,6 +1523,7 @@ 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"},
@@ -1470,6 +1535,7 @@ version = "6.29.5"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "ipykernel-6.29.5-py3-none-any.whl", hash = "sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5"},
     {file = "ipykernel-6.29.5.tar.gz", hash = "sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215"},
@@ -1503,6 +1569,7 @@ version = "8.28.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
+groups = ["main", "bngl"]
 files = [
     {file = "ipython-8.28.0-py3-none-any.whl", hash = "sha256:530ef1e7bb693724d3cdc37287c80b07ad9b25986c007a53aa1857272dac3f35"},
     {file = "ipython-8.28.0.tar.gz", hash = "sha256:0d0d15ca1e01faeb868ef56bc7ee5a0de5bd66885735682e8a322ae289a13d1a"},
@@ -1524,7 +1591,7 @@ typing-extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 [package.extras]
 all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx-registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "intersphinx-registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli ; python_version < \"3.11\"", "typing-extensions"]
 kernel = ["ipykernel"]
 matplotlib = ["matplotlib"]
 nbconvert = ["nbconvert"]
@@ -1541,6 +1608,7 @@ 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"},
@@ -1555,6 +1623,7 @@ version = "20.11.0"
 description = "Operations with ISO 8601 durations"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "isoduration-20.11.0-py3-none-any.whl", hash = "sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042"},
     {file = "isoduration-20.11.0.tar.gz", hash = "sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9"},
@@ -1569,6 +1638,7 @@ version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl"]
 files = [
     {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
     {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
@@ -1588,6 +1658,7 @@ version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl", "docs"]
 files = [
     {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
     {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
@@ -1605,6 +1676,7 @@ version = "0.9.25"
 description = "A Python implementation of the JSON5 data format."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "json5-0.9.25-py3-none-any.whl", hash = "sha256:34ed7d834b1341a86987ed52f3f76cd8ee184394906b6e22a1e0deb9ab294e8f"},
     {file = "json5-0.9.25.tar.gz", hash = "sha256:548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae"},
@@ -1616,6 +1688,7 @@ version = "3.0.0"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"},
     {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"},
@@ -1627,6 +1700,7 @@ version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "dev"]
 files = [
     {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
     {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
@@ -1656,6 +1730,7 @@ version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "bngl", "dev"]
 files = [
     {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"},
     {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"},
@@ -1670,6 +1745,7 @@ version = "8.6.3"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"},
     {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"},
@@ -1684,7 +1760,7 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-core"
@@ -1692,6 +1768,7 @@ version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"},
     {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"},
@@ -1712,6 +1789,7 @@ version = "0.10.0"
 description = "Jupyter Event System library"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyter_events-0.10.0-py3-none-any.whl", hash = "sha256:4b72130875e59d57716d327ea70d3ebc3af1944d3717e5a498b8a06c6c159960"},
     {file = "jupyter_events-0.10.0.tar.gz", hash = "sha256:670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22"},
@@ -1737,6 +1815,7 @@ version = "2.2.5"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"},
     {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"},
@@ -1751,6 +1830,7 @@ version = "2.14.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"},
     {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"},
@@ -1787,6 +1867,7 @@ version = "0.5.3"
 description = "A Jupyter Server Extension Providing Terminals."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"},
     {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"},
@@ -1806,6 +1887,7 @@ version = "4.2.5"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyterlab-4.2.5-py3-none-any.whl", hash = "sha256:73b6e0775d41a9fee7ee756c80f58a6bed4040869ccc21411dc559818874d321"},
     {file = "jupyterlab-4.2.5.tar.gz", hash = "sha256:ae7f3a1b8cb88b4f55009ce79fa7c06f99d70cd63601ee4aa91815d054f46f75"},
@@ -1840,6 +1922,7 @@ version = "0.3.0"
 description = "Pygments theme using JupyterLab CSS variables"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyterlab_pygments-0.3.0-py3-none-any.whl", hash = "sha256:841a89020971da1d8693f1a99997aefc5dc424bb1b251fd6322462a1b8842780"},
     {file = "jupyterlab_pygments-0.3.0.tar.gz", hash = "sha256:721aca4d9029252b11cfa9d185e5b5af4d54772bb8072f9b7036f4170054d35d"},
@@ -1851,6 +1934,7 @@ version = "2.27.3"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "jupyterlab_server-2.27.3-py3-none-any.whl", hash = "sha256:e697488f66c3db49df675158a77b3b017520d772c6e1548c7d9bcc5df7944ee4"},
     {file = "jupyterlab_server-2.27.3.tar.gz", hash = "sha256:eb36caca59e74471988f0ae25c77945610b887f777255aa21f8065def9e51ed4"},
@@ -1876,6 +1960,7 @@ 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"},
@@ -1895,6 +1980,7 @@ version = "1.4.7"
 description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "lems", "neuroml"]
 files = [
     {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8a9c83f75223d5e48b0bc9cb1bf2776cf01563e00ade8775ffe13b0b6e1af3a6"},
     {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:58370b1ffbd35407444d57057b57da5d6549d2d854fa30249771775c63b5fe17"},
@@ -2018,6 +2104,7 @@ version = "0.5.0"
 description = "libCellML Library: A library for the parsing, printing, and manipulation"
 optional = false
 python-versions = "*"
+groups = ["main", "cellml"]
 files = [
     {file = "libcellml-0.5.0-cp310-cp310-macosx_10_15_x86_64.whl", hash = "sha256:3583fb0c3b97a25031f8a44ac7f6719d51632e8f5799096649c91bca56f12170"},
     {file = "libcellml-0.5.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:4ab3a44b3d317411f24e3847394fcf270c8be4976f34ebb179a999d3e9a0df77"},
@@ -2049,6 +2136,7 @@ version = "0.6.5"
 description = "A Python library for working with NeuroML descriptions of neuronal models"
 optional = false
 python-versions = "*"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "libNeuroML-0.6.5-py3-none-any.whl", hash = "sha256:d62e079414ea484f76f45c7b682ebfa3fff288da6262e1a9672616fc8bb8ea58"},
     {file = "libneuroml-0.6.5.tar.gz", hash = "sha256:f54fecd1472069a72a0869714e98f0cf185e7a64c449ead86db627bb4118ece5"},
@@ -2063,7 +2151,7 @@ six = "*"
 tables = ">=3.3.0"
 
 [package.extras]
-dev = ["cython", "flake8", "generateds (>=2.20a)", "natsort", "networkx", "numpy (<2.0.0)", "pre-commit", "pytest", "ruff", "wheel"]
+dev = ["cython", "flake8", "generateds (>=2.20a) ; python_version >= \"3.0\"", "natsort", "networkx", "numpy (<2.0.0)", "pre-commit", "pytest", "ruff", "wheel"]
 doc = ["natsort", "pydata-sphinx-theme", "sphinxcontrib-bibtex"]
 full = ["libNeuroML[dev]", "libNeuroML[doc]", "libNeuroML[test]"]
 test = ["pytest"]
@@ -2074,6 +2162,7 @@ version = "2.7.0"
 description = "libRoadRunner: A simulation and analysis library for SBML"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "libroadrunner-2.7.0-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:71ed317ec218079a269b7aa53667c235b3e194abe68dff35e1d05b697b36bb53"},
     {file = "libroadrunner-2.7.0-cp310-cp310-macosx_14_0_arm64.whl", hash = "sha256:b6e2ea3e9f25f8f7c48f2e0fccbfe14f86f169eca610fe2ccc1349418f95497d"},
@@ -2106,6 +2195,7 @@ 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", "bngl", "lems", "neuroml"]
 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"},
@@ -2260,6 +2350,7 @@ version = "3.0.1"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "bngl", "docs"]
 files = [
     {file = "MarkupSafe-3.0.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:db842712984e91707437461930e6011e60b39136c7331e971952bb30465bc1a1"},
     {file = "MarkupSafe-3.0.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:3ffb4a8e7d46ed96ae48805746755fadd0909fea2306f93d5d8233ba23dda12a"},
@@ -2330,6 +2421,7 @@ version = "3.9.2"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "bngl", "lems", "neuroml"]
 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"},
@@ -2393,6 +2485,7 @@ version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"},
     {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"},
@@ -2407,6 +2500,7 @@ version = "0.8.1"
 description = "Artist for matplotlib to display a scale bar"
 optional = false
 python-versions = "~=3.7"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "matplotlib-scalebar-0.8.1.tar.gz", hash = "sha256:14887af1093579c5e6afae51a0a1ecc3f715cdbc5c4d7ef59cdeec76ee6bb15d"},
     {file = "matplotlib_scalebar-0.8.1-py2.py3-none-any.whl", hash = "sha256:a8a2f361d4c2d576d087df3092ed95cac2f708f8b40d5d2bb992bd190e740b3a"},
@@ -2421,6 +2515,7 @@ version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
 optional = false
 python-versions = ">=3.6"
+groups = ["dev"]
 files = [
     {file = "mccabe-0.7.0-py2.py3-none-any.whl", hash = "sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e"},
     {file = "mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325"},
@@ -2432,6 +2527,7 @@ version = "3.0.2"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "mistune-3.0.2-py3-none-any.whl", hash = "sha256:71481854c30fdbc938963d3605b72501f5c10a9320ecd412c121c163a1c7d205"},
     {file = "mistune-3.0.2.tar.gz", hash = "sha256:fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8"},
@@ -2443,6 +2539,7 @@ version = "0.3.5"
 description = "A common JSON/YAML based format for compact model specification"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "modelspec-0.3.5-py3-none-any.whl", hash = "sha256:6e49e190113f7a0e205867bbe4a26c713acb17f62d287ccfd880203bade9a122"},
     {file = "modelspec-0.3.5.tar.gz", hash = "sha256:b4f0f449e376d5edbb36179ae383faeb6749b4630735fe0ab13acbe36c6d7462"},
@@ -2461,7 +2558,7 @@ tabulate = "*"
 all = ["modelspec[dev]", "modelspec[docs]", "modelspec[test]"]
 dev = ["NeuroMLlite (>=0.5.3)", "flake8", "modelspec[test]", "pre-commit", "pyneuroml (>=0.7.2)", "python-libsbml"]
 docs = ["Sphinx", "myst-parser", "nbsphinx", "pandas", "pytorch-sphinx-theme (==0.0.19)", "recommonmark (>=0.5.0)", "requests", "sphinx-autoapi", "sphinx-copybutton", "sphinx-markdown-tables", "sphinx-rtd-theme", "sphinxcontrib-versioning"]
-test = ["pytest", "pytest-benchmark", "pytest-mock", "typing-extensions"]
+test = ["pytest", "pytest-benchmark", "pytest-mock", "typing-extensions ; python_version < \"3.8\""]
 
 [[package]]
 name = "mpmath"
@@ -2469,6 +2566,7 @@ version = "1.3.0"
 description = "Python library for arbitrary-precision floating-point arithmetic"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl", "lems", "neuroml"]
 files = [
     {file = "mpmath-1.3.0-py3-none-any.whl", hash = "sha256:a0b2b9fe80bbcd81a6647ff13108738cfb482d481d826cc0e02f5b35e5c88d2c"},
     {file = "mpmath-1.3.0.tar.gz", hash = "sha256:7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f"},
@@ -2477,7 +2575,7 @@ 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]]
@@ -2486,6 +2584,7 @@ version = "1.1.0"
 description = "MessagePack serializer"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "msgpack-1.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7ad442d527a7e358a469faf43fda45aaf4ac3249c8310a82f0ccff9164e5dccd"},
     {file = "msgpack-1.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:74bed8f63f8f14d75eec75cf3d04ad581da6b914001b474a5d3cd3372c8cc27d"},
@@ -2559,6 +2658,7 @@ version = "8.4.0"
 description = "Simple yet flexible natural sorting in Python."
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "natsort-8.4.0-py3-none-any.whl", hash = "sha256:4732914fb471f56b5cce04d7bae6f164a592c7712e1c85f9ef585e197299521c"},
     {file = "natsort-8.4.0.tar.gz", hash = "sha256:45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581"},
@@ -2574,6 +2674,7 @@ version = "0.10.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
 python-versions = ">=3.8.0"
+groups = ["main", "bngl"]
 files = [
     {file = "nbclient-0.10.0-py3-none-any.whl", hash = "sha256:f13e3529332a1f1f81d82a53210322476a168bb7090a0289c795fe9cc11c9d3f"},
     {file = "nbclient-0.10.0.tar.gz", hash = "sha256:4b3f1b7dba531e498449c4db4f53da339c91d449dc11e9af3a43b4eb5c5abb09"},
@@ -2596,6 +2697,7 @@ version = "7.16.4"
 description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"},
     {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"},
@@ -2633,6 +2735,7 @@ version = "5.10.4"
 description = "The Jupyter Notebook format"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"},
     {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"},
@@ -2654,6 +2757,7 @@ version = "0.7"
 description = "Open a notebook from the command line in the best available server"
 optional = false
 python-versions = ">=3.5"
+groups = ["main", "bngl"]
 files = [
     {file = "nbopen-0.7-py3-none-any.whl", hash = "sha256:5266be9ab81ce541f040698c3c6b99fdd22b0df2b334daa5cf2179e1a2553c64"},
     {file = "nbopen-0.7.tar.gz", hash = "sha256:1c80ed2d80da0245270b4de9d2a1a44b19e55cfa17348ac45ee3d6f076303503"},
@@ -2669,6 +2773,7 @@ version = "1.9.2"
 description = "A Python library for manipulating indices of ndarrays."
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "ndindex-1.9.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6c0bd9fb02b5ac6e3e8b70404930e1f6824ad565363bf8f0e817d6f6a3a47593"},
     {file = "ndindex-1.9.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:3502df515c225e653b55fc08e714d4ae56306ad46454759d90156530cb4e2f40"},
@@ -2732,6 +2837,7 @@ version = "1.6.0"
 description = "Patch asyncio to allow nested event loops"
 optional = false
 python-versions = ">=3.5"
+groups = ["main", "bngl"]
 files = [
     {file = "nest_asyncio-1.6.0-py3-none-any.whl", hash = "sha256:87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c"},
     {file = "nest_asyncio-1.6.0.tar.gz", hash = "sha256:6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe"},
@@ -2743,6 +2849,7 @@ version = "3.3"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
 python-versions = ">=3.10"
+groups = ["main", "bngl", "lems", "neuroml"]
 files = [
     {file = "networkx-3.3-py3-none-any.whl", hash = "sha256:28575580c6ebdaf4505b22c6256a2b9de86b316dc63ba9e93abde3d78dfdbcf2"},
     {file = "networkx-3.3.tar.gz", hash = "sha256:0c127d8b2f4865f59ae9cb8aafcd60b5c70f3241ebd66f7defad7c4ab90126c9"},
@@ -2761,6 +2868,7 @@ version = "0.6.0"
 description = "A common JSON/YAML based format for compact network specification, closely tied to NeuroML v2"
 optional = false
 python-versions = "*"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "neuromllite-0.6.0-py3-none-any.whl", hash = "sha256:69957f04bf8ce14a259fa67f4530df3efd0e3be4381123a9ae79b99bbf5e7247"},
     {file = "neuromllite-0.6.0.tar.gz", hash = "sha256:615a81cf6611cedb206ba5291a61772e4f182d74798f3fdb3d49bbb55019fd79"},
@@ -2781,6 +2889,7 @@ version = "7.2.2"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "notebook-7.2.2-py3-none-any.whl", hash = "sha256:c89264081f671bc02eec0ed470a627ed791b9156cad9285226b31611d3e9fe1c"},
     {file = "notebook-7.2.2.tar.gz", hash = "sha256:2ef07d4220421623ad3fe88118d687bc0450055570cdd160814a59cf3a1c516e"},
@@ -2796,7 +2905,7 @@ tornado = ">=6.2.0"
 [package.extras]
 dev = ["hatch", "pre-commit"]
 docs = ["myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx (>=1.3.6)", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
+test = ["importlib-resources (>=5.0) ; python_version < \"3.10\"", "ipykernel", "jupyter-server[test] (>=2.4.0,<3)", "jupyterlab-server[test] (>=2.27.1,<3)", "nbval", "pytest (>=7.0)", "pytest-console-scripts", "pytest-timeout", "pytest-tornasync", "requests"]
 
 [[package]]
 name = "notebook-shim"
@@ -2804,6 +2913,7 @@ version = "0.2.4"
 description = "A shim layer for notebook traits and config"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "notebook_shim-0.2.4-py3-none-any.whl", hash = "sha256:411a5be4e9dc882a074ccbcae671eda64cceb068767e9a3419096986560e1cef"},
     {file = "notebook_shim-0.2.4.tar.gz", hash = "sha256:b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb"},
@@ -2821,6 +2931,7 @@ version = "2.10.1"
 description = "Fast numerical expression evaluator for NumPy"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "numexpr-2.10.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bbd35f17f6efc00ebd4a480192af1ee30996094a0d5343b131b0e90e61e8b554"},
     {file = "numexpr-2.10.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:fecdf4bf3c1250e56583db0a4a80382a259ba4c2e1efa13e04ed43f0938071f5"},
@@ -2862,6 +2973,7 @@ version = "1.26.4"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "bngl", "dev", "escher", "lems", "neuroml", "simularium"]
 files = [
     {file = "numpy-1.26.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9ff0f4f29c51e2803569d7a51c2304de5554655a60c5d776e35b4a41413830d0"},
     {file = "numpy-1.26.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2e4ee3380d6de9c9ec04745830fd9e2eccb3e6cf790d39d7b98ffd19b0dd754a"},
@@ -2907,6 +3019,7 @@ 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"},
@@ -2921,6 +3034,7 @@ version = "7.7.0"
 description = "A decorator to automatically detect mismatch when overriding a method."
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl"]
 files = [
     {file = "overrides-7.7.0-py3-none-any.whl", hash = "sha256:c7ed9d062f78b8e4c1a7b70bd8796b35ead4d9f510227ef9c5dc7626c60d7e49"},
     {file = "overrides-7.7.0.tar.gz", hash = "sha256:55158fa3d93b98cc75299b1e67078ad9003ca27945c76162c1c0766d6f91820a"},
@@ -2932,6 +3046,7 @@ version = "24.1"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "dev", "docs", "lems", "neuroml"]
 files = [
     {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"},
     {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
@@ -2943,6 +3058,7 @@ version = "2.2.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "bngl", "simularium"]
 files = [
     {file = "pandas-2.2.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1948ddde24197a0f7add2bdc4ca83bf2b1ef84a1bc8ccffd95eda17fd836ecb5"},
     {file = "pandas-2.2.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:381175499d3802cde0eabbaf6324cce0c4f5d52ca6f8c377c29ad442f50f6348"},
@@ -3029,6 +3145,7 @@ version = "1.5.1"
 description = "Utilities for writing pandoc filters in python"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+groups = ["main", "bngl"]
 files = [
     {file = "pandocfilters-1.5.1-py2.py3-none-any.whl", hash = "sha256:93be382804a9cdb0a7267585f157e5d1731bbe5545a85b268d6f5fe6232de2bc"},
     {file = "pandocfilters-1.5.1.tar.gz", hash = "sha256:002b4a555ee4ebc03f8b66307e287fa492e4a77b4ea14d3f934328297bb4939e"},
@@ -3040,6 +3157,7 @@ version = "0.8.4"
 description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl"]
 files = [
     {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"},
     {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"},
@@ -3055,6 +3173,8 @@ version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
+markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""
 files = [
     {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"},
     {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"},
@@ -3069,6 +3189,7 @@ version = "10.4.0"
 description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "lems", "neuroml"]
 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"},
@@ -3157,7 +3278,7 @@ 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]]
@@ -3166,6 +3287,7 @@ version = "0.24.3"
 description = "Physical quantities module"
 optional = false
 python-versions = ">=3.9"
+groups = ["main", "lems", "simularium"]
 files = [
     {file = "Pint-0.24.3-py3-none-any.whl", hash = "sha256:d98667e46fd03a1b94694fbfa104ec30858684d8ab26952e2a348b48059089bb"},
     {file = "pint-0.24.3.tar.gz", hash = "sha256:d54771093e8b94c4e0a35ac638c2444ddf3ef685652bab7675ffecfa0c5c5cdf"},
@@ -3195,6 +3317,7 @@ version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "platformdirs-4.3.6-py3-none-any.whl", hash = "sha256:73e575e1408ab8103900836b97580d5307456908a03e92031bab39e4554cc3fb"},
     {file = "platformdirs-4.3.6.tar.gz", hash = "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907"},
@@ -3211,6 +3334,7 @@ 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"},
@@ -3226,6 +3350,7 @@ version = "1.7.6.9"
 description = "distributed and parallel Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "ppft-1.7.6.9-py3-none-any.whl", hash = "sha256:dab36548db5ca3055067fbe6b1a17db5fee29f3c366c579a9a27cebb52ed96f0"},
     {file = "ppft-1.7.6.9.tar.gz", hash = "sha256:73161c67474ea9d81d04bcdad166d399cff3f084d5d2dc21ebdd46c075bbc265"},
@@ -3243,6 +3368,7 @@ version = "4.5.0"
 description = "A Python Progressbar library to provide visual (yet text based) progress to long running operations."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "progressbar2-4.5.0-py3-none-any.whl", hash = "sha256:625c94a54e63915b3959355e6d4aacd63a00219e5f3e2b12181b76867bf6f628"},
     {file = "progressbar2-4.5.0.tar.gz", hash = "sha256:6662cb624886ed31eb94daf61e27583b5144ebc7383a17bae076f8f4f59088fb"},
@@ -3253,7 +3379,7 @@ python-utils = ">=3.8.1"
 
 [package.extras]
 docs = ["sphinx (>=1.8.5)", "sphinx-autodoc-typehints (>=1.6.0)"]
-tests = ["dill (>=0.3.6)", "flake8 (>=3.7.7)", "freezegun (>=0.3.11)", "pytest (>=4.6.9)", "pytest-cov (>=2.6.1)", "pytest-mypy", "pywin32", "sphinx (>=1.8.5)"]
+tests = ["dill (>=0.3.6)", "flake8 (>=3.7.7)", "freezegun (>=0.3.11)", "pytest (>=4.6.9)", "pytest-cov (>=2.6.1)", "pytest-mypy", "pywin32 ; sys_platform == \"win32\"", "sphinx (>=1.8.5)"]
 
 [[package]]
 name = "prometheus-client"
@@ -3261,6 +3387,7 @@ version = "0.21.0"
 description = "Python client for the Prometheus monitoring system."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "prometheus_client-0.21.0-py3-none-any.whl", hash = "sha256:4fa6b4dd0ac16d58bb587c04b1caae65b8c5043e85f778f42f5f632f6af2e166"},
     {file = "prometheus_client-0.21.0.tar.gz", hash = "sha256:96c83c606b71ff2b0a433c98889d275f51ffec6c5e267de37c7a2b5c9aa9233e"},
@@ -3275,6 +3402,7 @@ version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.7.0"
+groups = ["main", "bngl"]
 files = [
     {file = "prompt_toolkit-3.0.48-py3-none-any.whl", hash = "sha256:f49a827f90062e411f1ce1f854f2aedb3c23353244f8108b89283587397ac10e"},
     {file = "prompt_toolkit-3.0.48.tar.gz", hash = "sha256:d6623ab0477a80df74e646bdbc93621143f5caf104206aa29294d53de1a03d90"},
@@ -3289,6 +3417,7 @@ version = "2.5.8"
 description = "Python frontend to ontologies."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "pronto-2.5.8-py2.py3-none-any.whl", hash = "sha256:91445cd2c2000729e9b23be47b1e142fd967239700284f1375ee2b78d54a3416"},
     {file = "pronto-2.5.8.tar.gz", hash = "sha256:5283ec5b35ddc12d34f2e50098b9900bb7b80172b7f769ccc93f5d82b7022799"},
@@ -3306,6 +3435,7 @@ version = "6.0.0"
 description = "Cross-platform lib for process and system monitoring in Python."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+groups = ["main", "bngl"]
 files = [
     {file = "psutil-6.0.0-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:a021da3e881cd935e64a3d0a20983bda0bb4cf80e4f74fa9bfcb1bc5785360c6"},
     {file = "psutil-6.0.0-cp27-cp27m-manylinux2010_i686.whl", hash = "sha256:1287c2b95f1c0a364d23bc6f2ea2365a8d4d9b726a3be7294296ff7ba97c17f0"},
@@ -3327,7 +3457,7 @@ files = [
 ]
 
 [package.extras]
-test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
+test = ["enum34 ; python_version <= \"3.4\"", "ipaddress ; python_version < \"3.0\"", "mock ; python_version < \"3.0\"", "pywin32 ; sys_platform == \"win32\"", "wmi ; sys_platform == \"win32\""]
 
 [[package]]
 name = "ptyprocess"
@@ -3335,6 +3465,8 @@ version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
+markers = "os_name != \"nt\" or sys_platform != \"win32\" and sys_platform != \"emscripten\""
 files = [
     {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"},
     {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"},
@@ -3346,6 +3478,7 @@ version = "0.2.3"
 description = "Safely evaluate AST nodes without side effects"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"},
     {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"},
@@ -3360,6 +3493,7 @@ version = "9.0.0"
 description = "Get CPU info with pure Python"
 optional = false
 python-versions = "*"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "py-cpuinfo-9.0.0.tar.gz", hash = "sha256:3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690"},
     {file = "py_cpuinfo-9.0.0-py3-none-any.whl", hash = "sha256:859625bc251f64e21f077d099d4162689c762b5d6a4c3c97553d56241c9674d5"},
@@ -3371,6 +3505,7 @@ version = "2.12.1"
 description = "Python style guide checker"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pycodestyle-2.12.1-py2.py3-none-any.whl", hash = "sha256:46f0fb92069a7c28ab7bb558f05bfc0110dac69a0cd23c61ea0040283a9d78b3"},
     {file = "pycodestyle-2.12.1.tar.gz", hash = "sha256:6838eae08bbce4f6accd5d5572075c63626a15ee3e6f842df996bf62f6d73521"},
@@ -3382,6 +3517,7 @@ version = "2.22"
 description = "C parser in Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"},
     {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"},
@@ -3393,6 +3529,7 @@ version = "0.15.4"
 description = "Bootstrap-based Sphinx theme from the PyData community"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 files = [
     {file = "pydata_sphinx_theme-0.15.4-py3-none-any.whl", hash = "sha256:2136ad0e9500d0949f96167e63f3e298620040aea8f9c74621959eda5d4cf8e6"},
     {file = "pydata_sphinx_theme-0.15.4.tar.gz", hash = "sha256:7762ec0ac59df3acecf49fd2f889e1b4565dbce8b88b2e29ee06fdd90645a06d"},
@@ -3421,6 +3558,7 @@ version = "3.0.2"
 description = "Python interface to Graphviz's Dot"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "pydot-3.0.2-py3-none-any.whl", hash = "sha256:99cedaa55d04abb0b2bc56d9981a6da781053dd5ac75c428e8dd53db53f90b14"},
     {file = "pydot-3.0.2.tar.gz", hash = "sha256:9180da540b51b3aa09fbf81140b3edfbe2315d778e8589a7d0a4a69c41332bae"},
@@ -3440,6 +3578,7 @@ version = "3.2.0"
 description = "passive checker of Python programs"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pyflakes-3.2.0-py2.py3-none-any.whl", hash = "sha256:84b5be138a2dfbb40689ca07e2152deb896a65c3a3e24c251c5c62489568074a"},
     {file = "pyflakes-3.2.0.tar.gz", hash = "sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f"},
@@ -3451,6 +3590,7 @@ version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "docs"]
 files = [
     {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"},
     {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"},
@@ -3465,6 +3605,7 @@ version = "0.6.7"
 description = "A Python library for working with the Low Entropy Model Specification language (LEMS)"
 optional = false
 python-versions = "*"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "PyLEMS-0.6.7-py3-none-any.whl", hash = "sha256:ba066a3406c5cba264e758338c7143571f3157323566208b3f3c10a3be32e7d4"},
     {file = "PyLEMS-0.6.7.tar.gz", hash = "sha256:b82b66dbe51206b6c3db915651aadfeb6e8eeb5a95d3114ca8b97725f2fafce6"},
@@ -3482,6 +3623,7 @@ version = "1.2.1"
 description = "A least recently used (LRU) cache implementation"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "pylru-1.2.1-py3-none-any.whl", hash = "sha256:b7c75b0676e2fbae647823bc209e23998772867d3679f1583c7350a9b02a59f0"},
     {file = "pylru-1.2.1.tar.gz", hash = "sha256:47ad140a63ab9389648dadfbb4330700e0ffeeb28ec04664ee47d37ed133b0f4"},
@@ -3493,6 +3635,7 @@ version = "4.10.1"
 description = "Python driver for MongoDB <http://www.mongodb.org>"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "pymongo-4.10.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e699aa68c4a7dea2ab5a27067f7d3e08555f8d2c0dc6a0c8c60cfd9ff2e6a4b1"},
     {file = "pymongo-4.10.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:70645abc714f06b4ad6b72d5bf73792eaad14e3a2cfe29c62a9c81ada69d9e4b"},
@@ -3561,9 +3704,9 @@ dnspython = ">=1.16.0,<3.0.0"
 [package.extras]
 aws = ["pymongo-auth-aws (>=1.1.0,<2.0.0)"]
 docs = ["furo (==2023.9.10)", "readthedocs-sphinx-search (>=0.3,<1.0)", "sphinx (>=5.3,<8)", "sphinx-autobuild (>=2020.9.1)", "sphinx-rtd-theme (>=2,<3)", "sphinxcontrib-shellcheck (>=1,<2)"]
-encryption = ["certifi", "pymongo-auth-aws (>=1.1.0,<2.0.0)", "pymongocrypt (>=1.10.0,<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)"]
+encryption = ["certifi ; os_name == \"nt\" or sys_platform == \"darwin\"", "pymongo-auth-aws (>=1.1.0,<2.0.0)", "pymongocrypt (>=1.10.0,<2.0.0)"]
+gssapi = ["pykerberos ; os_name != \"nt\"", "winkerberos (>=0.5.0) ; os_name == \"nt\""]
+ocsp = ["certifi ; os_name == \"nt\" or sys_platform == \"darwin\"", "cryptography (>=2.5)", "pyopenssl (>=17.2.0)", "requests (<3.0.0)", "service-identity (>=18.1.0)"]
 snappy = ["python-snappy"]
 test = ["pytest (>=8.2)", "pytest-asyncio (>=0.24.0)"]
 zstd = ["zstandard"]
@@ -3574,6 +3717,7 @@ version = "1.3.12"
 description = "Python utilities for NeuroML"
 optional = false
 python-versions = "*"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "pyNeuroML-1.3.12-py3-none-any.whl", hash = "sha256:e2ad6c21af03815139a8200d63ef1edb5d519016261e3defff824722c348bd2f"},
     {file = "pyneuroml-1.3.12.tar.gz", hash = "sha256:9aa3b5d53852b5102934200d5a0a763b58592dc5606c78df3d628d1adbcae62e"},
@@ -3611,7 +3755,7 @@ povray = ["opencv-python"]
 tellurium = ["tellurium"]
 tune = ["neurotune (>=0.2.6)"]
 vispy = ["pyNeuroML[vispy-common]", "pyqt6"]
-vispy-common = ["PyOpenGL-accelerate", "frozendict", "pyopengl", "scikit-learn", "scipy", "vispy (>=0.13.0)"]
+vispy-common = ["PyOpenGL-accelerate ; python_version < \"3.12\"", "frozendict", "pyopengl", "scikit-learn", "scipy", "vispy (>=0.13.0)"]
 vispy-qt5 = ["pyNeuroML[vispy-common]", "pyqt5"]
 
 [[package]]
@@ -3620,6 +3764,7 @@ 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"},
@@ -3650,6 +3795,7 @@ 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", "bngl", "lems", "neuroml"]
 files = [
     {file = "pyparsing-3.1.4-py3-none-any.whl", hash = "sha256:a6a7ee4235a3f944aa1fa2249307708f893fe5717dc603503c6c7969c070fb7c"},
     {file = "pyparsing-3.1.4.tar.gz", hash = "sha256:f86ec8d1a83f11977c9a6ea7598e8c27fc5cddfa5b07ea2241edbbde1d7bc032"},
@@ -3664,6 +3810,8 @@ version = "3.5.4"
 description = "A python implementation of GNU readline."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "dev", "logging"]
+markers = "sys_platform == \"win32\""
 files = [
     {file = "pyreadline3-3.5.4-py3-none-any.whl", hash = "sha256:eaf8e6cc3c49bcccf145fc6067ba8643d1df34d604a1ec0eccbf7a18e6d3fae6"},
     {file = "pyreadline3-3.5.4.tar.gz", hash = "sha256:8d57d53039a1c75adba8e50dd3d992b28143480816187ea5efbd5c78e6c885b7"},
@@ -3678,6 +3826,7 @@ version = "8.3.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pytest-8.3.3-py3-none-any.whl", hash = "sha256:a6853c7375b2663155079443d2e45de913a911a11d669df02a50814944db57b2"},
     {file = "pytest-8.3.3.tar.gz", hash = "sha256:70b98107bd648308a7952b06e6ca9a50bc660be218d53c257cc1fc94fda10181"},
@@ -3700,6 +3849,7 @@ version = "5.0.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "pytest-cov-5.0.0.tar.gz", hash = "sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857"},
     {file = "pytest_cov-5.0.0-py3-none-any.whl", hash = "sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652"},
@@ -3718,6 +3868,7 @@ 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", "bngl", "lems", "neuroml", "simularium"]
 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"},
@@ -3732,6 +3883,7 @@ version = "2.0.7"
 description = "A python library adding a json log formatter"
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "bngl"]
 files = [
     {file = "python-json-logger-2.0.7.tar.gz", hash = "sha256:23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c"},
     {file = "python_json_logger-2.0.7-py3-none-any.whl", hash = "sha256:f380b826a991ebbe3de4d897aeec42760035ac760345e57b812938dc8b35e2bd"},
@@ -3743,6 +3895,7 @@ 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"},
@@ -3769,6 +3922,14 @@ 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"},
@@ -3800,6 +3961,7 @@ version = "5.20.4"
 description = "LibSBML Python API"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl", "sbml"]
 files = [
     {file = "python_libsbml-5.20.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2c7a271cdaef200fe66f92ceefb85bb0dc647fa4fe966cec84af7efb685e93fd"},
     {file = "python_libsbml-5.20.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a69d9130148fc7aa85b4c42f804c6111c167711d39ed3a64145d15cb0296ec57"},
@@ -3828,6 +3990,14 @@ files = [
     {file = "python_libsbml-5.20.4-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:b1ef224f746aac4e1b0f917113b6334abd2fa3eb63bde41149a1b006bacfba81"},
     {file = "python_libsbml-5.20.4-cp312-cp312-win32.whl", hash = "sha256:b5cc68b5fe6d139a4557cba9d9913b3e196582bdb7975bea6a2c25faaecdfadb"},
     {file = "python_libsbml-5.20.4-cp312-cp312-win_amd64.whl", hash = "sha256:40c5e9ec86c467b4f325b5365ca369ecc1c9ced608e390d3cc1726f79da68968"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:233c01e17a0750ea73411ce79b069bf113968cabeb88d61fc9378d068c4c585c"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:6e8c99146b15b0c5c9aabb6ec85e30489a1b8105cf7d2483b44e0407d7d04309"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:cde96e40eb6809de40443e28f8242674842e2cfbb9c84d2c28321f553fbd344e"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3ff1eb26b1d39531c80813ed9c18f9dc6aca66e437a81131bd0ed1c97371df11"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:576d6a64d3bd04803db160d992b7e6ac9be4bc2ba735a3a33fa623ca4e86fe09"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:2c0d0eddb043a5065abead423dec089d99191727a0f6505ddd2c942512a4307d"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-win32.whl", hash = "sha256:1c5539b2189e38e5b39c34eafe1ef86ffb9179ece91c48623a48412cb88a6f5c"},
+    {file = "python_libsbml-5.20.4-cp313-cp313-win_amd64.whl", hash = "sha256:aac5a989e24341713e3c2fd126c6deebdb062adb287b41a45c48c72a4bd828ca"},
     {file = "python_libsbml-5.20.4-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:feeecfffa72f94ac74475180f1046feb019b30ec86f9ef435c31e4585a0762f4"},
     {file = "python_libsbml-5.20.4-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4bd57cc81dc508c42c0bed66e6aed67b8dc2d3b56802d56192be418bf032a175"},
     {file = "python_libsbml-5.20.4-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:56402db093a38adb35b985a0c31b8875b360aeba04f29e5675be9a691a6911bf"},
@@ -3861,6 +4031,7 @@ 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"},
@@ -3888,6 +4059,14 @@ 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"},
@@ -3926,6 +4105,7 @@ version = "3.9.0"
 description = "Python Utils is a module with some convenient utilities not included with the standard Python install"
 optional = false
 python-versions = ">3.9.0"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "python_utils-3.9.0-py2.py3-none-any.whl", hash = "sha256:a7719a5ef4bae7360d2a15c13b08c4e3c3e39b9df19bd16f119ff8d0cfeaafb7"},
     {file = "python_utils-3.9.0.tar.gz", hash = "sha256:3689556884e3ae53aec5a4c9f17b36e752a3e93a7ba2768c6553fc4dd6fa70ef"},
@@ -3945,6 +4125,7 @@ version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl", "simularium"]
 files = [
     {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"},
     {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"},
@@ -3956,6 +4137,7 @@ version = "307"
 description = "Python for Window Extensions"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl", "containers", "dev"]
 files = [
     {file = "pywin32-307-cp310-cp310-win32.whl", hash = "sha256:f8f25d893c1e1ce2d685ef6d0a481e87c6f510d0f3f117932781f412e0eba31b"},
     {file = "pywin32-307-cp310-cp310-win_amd64.whl", hash = "sha256:36e650c5e5e6b29b5d317385b02d20803ddbac5d1031e1f88d20d76676dd103d"},
@@ -3976,6 +4158,7 @@ files = [
     {file = "pywin32-307-cp39-cp39-win32.whl", hash = "sha256:55ee87f2f8c294e72ad9d4261ca423022310a6e79fb314a8ca76ab3f493854c6"},
     {file = "pywin32-307-cp39-cp39-win_amd64.whl", hash = "sha256:e9d5202922e74985b037c9ef46778335c102b74b95cec70f629453dbe7235d87"},
 ]
+markers = {main = "sys_platform == \"win32\"", bngl = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\"", containers = "sys_platform == \"win32\"", dev = "sys_platform == \"win32\""}
 
 [[package]]
 name = "pywinpty"
@@ -3983,6 +4166,8 @@ version = "2.0.13"
 description = "Pseudo terminal support for Windows from Python."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
+markers = "os_name == \"nt\""
 files = [
     {file = "pywinpty-2.0.13-cp310-none-win_amd64.whl", hash = "sha256:697bff211fb5a6508fee2dc6ff174ce03f34a9a233df9d8b5fe9c8ce4d5eaf56"},
     {file = "pywinpty-2.0.13-cp311-none-win_amd64.whl", hash = "sha256:b96fb14698db1284db84ca38c79f15b4cfdc3172065b5137383910567591fa99"},
@@ -3998,6 +4183,7 @@ version = "6.0.2"
 description = "YAML parser and emitter for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "lems", "neuroml"]
 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"},
@@ -4060,6 +4246,7 @@ version = "26.2.0"
 description = "Python bindings for 0MQ"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:ddf33d97d2f52d89f6e6e7ae66ee35a4d9ca6f36eda89c24591b0c40205a3629"},
     {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dacd995031a01d16eec825bf30802fceb2c3791ef24bcce48fa98ce40918c27b"},
@@ -4181,6 +4368,7 @@ version = "7.0.0"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
 optional = false
 python-versions = ">=3.8.1,<4.0.0"
+groups = ["main"]
 files = [
     {file = "rdflib-7.0.0-py3-none-any.whl", hash = "sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd"},
     {file = "rdflib-7.0.0.tar.gz", hash = "sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae"},
@@ -4202,6 +4390,7 @@ version = "0.35.1"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "dev"]
 files = [
     {file = "referencing-0.35.1-py3-none-any.whl", hash = "sha256:eda6d3234d62814d1c64e305c1331c9a3a6132da475ab6382eaa997b21ee75de"},
     {file = "referencing-0.35.1.tar.gz", hash = "sha256:25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c"},
@@ -4217,6 +4406,7 @@ version = "2024.9.11"
 description = "Alternative regular expression module, to replace re."
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "regex-2024.9.11-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:1494fa8725c285a81d01dc8c06b55287a1ee5e0e382d8413adc0a9197aac6408"},
     {file = "regex-2024.9.11-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0e12c481ad92d129c78f13a2a3662317e46ee7ef96c94fd332e1c29131875b7d"},
@@ -4320,6 +4510,7 @@ version = "2.32.3"
 description = "Python HTTP for Humans."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "containers", "dev", "docs"]
 files = [
     {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"},
     {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"},
@@ -4341,6 +4532,7 @@ version = "0.1.4"
 description = "A pure python RFC3339 validator"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main", "bngl"]
 files = [
     {file = "rfc3339_validator-0.1.4-py2.py3-none-any.whl", hash = "sha256:24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa"},
     {file = "rfc3339_validator-0.1.4.tar.gz", hash = "sha256:138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b"},
@@ -4355,6 +4547,7 @@ version = "0.1.1"
 description = "Pure python rfc3986 validator"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["main", "bngl"]
 files = [
     {file = "rfc3986_validator-0.1.1-py2.py3-none-any.whl", hash = "sha256:2f235c432ef459970b4306369336b9d5dbdda31b510ca1e327636e01f528bfa9"},
     {file = "rfc3986_validator-0.1.1.tar.gz", hash = "sha256:3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055"},
@@ -4366,6 +4559,7 @@ version = "0.20.0"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "dev"]
 files = [
     {file = "rpds_py-0.20.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:3ad0fda1635f8439cde85c700f964b23ed5fc2d28016b32b9ee5fe30da5c84e2"},
     {file = "rpds_py-0.20.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9bb4a0d90fdb03437c109a17eade42dfbf6190408f29b2744114d11586611d6f"},
@@ -4478,6 +4672,7 @@ version = "0.13.2"
 description = "Statistical data visualization"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "seaborn-0.13.2-py3-none-any.whl", hash = "sha256:636f8336facf092165e27924f223d3c62ca560b1f2bb5dff7ab7fad265361987"},
     {file = "seaborn-0.13.2.tar.gz", hash = "sha256:93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7"},
@@ -4499,15 +4694,16 @@ version = "1.8.3"
 description = "Send file to trash natively under Mac OS X, Windows and Linux"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+groups = ["main", "bngl"]
 files = [
     {file = "Send2Trash-1.8.3-py3-none-any.whl", hash = "sha256:0c31227e0bd08961c7665474a3d1ef7193929fedda4233843689baa056be46c9"},
     {file = "Send2Trash-1.8.3.tar.gz", hash = "sha256:b18e7a3966d99871aefeb00cfbcfdced55ce4871194810fc71f4aa484b953abf"},
 ]
 
 [package.extras]
-nativelib = ["pyobjc-framework-Cocoa", "pywin32"]
-objc = ["pyobjc-framework-Cocoa"]
-win32 = ["pywin32"]
+nativelib = ["pyobjc-framework-Cocoa ; sys_platform == \"darwin\"", "pywin32 ; sys_platform == \"win32\""]
+objc = ["pyobjc-framework-Cocoa ; sys_platform == \"darwin\""]
+win32 = ["pywin32 ; sys_platform == \"win32\""]
 
 [[package]]
 name = "setuptools"
@@ -4515,19 +4711,20 @@ version = "75.1.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "setuptools-75.1.0-py3-none-any.whl", hash = "sha256:35ab7fd3bcd95e6b7fd704e4a1539513edad446c097797f2985e0e4b960772f2"},
     {file = "setuptools-75.1.0.tar.gz", hash = "sha256:d59a21b17a275fb872a9c3dae73963160ae079f1049ed956880cd7c09b120538"},
 ]
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.5.2)"]
-core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\"", "ruff (>=0.5.2) ; sys_platform != \"cygwin\""]
+core = ["importlib-metadata (>=6) ; python_version < \"3.10\"", "importlib-resources (>=5.10.2) ; python_version < \"3.9\"", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1) ; python_version < \"3.11\"", "wheel (>=0.43.0)"]
 cover = ["pytest-cov"]
 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)"]
 enabler = ["pytest-enabler (>=2.2)"]
-test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
-type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.11.*)", "pytest-mypy"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "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", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf ; sys_platform != \"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
+type = ["importlib-metadata (>=7.0.2) ; python_version < \"3.10\"", "jaraco.develop (>=7.21) ; sys_platform != \"cygwin\"", "mypy (==1.11.*)", "pytest-mypy"]
 
 [[package]]
 name = "simplejson"
@@ -4535,6 +4732,7 @@ 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"},
@@ -4654,6 +4852,7 @@ 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", "simularium"]
 files = [
     {file = "simulariumio-1.11.0-py3-none-any.whl", hash = "sha256:a23026e8ad650d88478094cfa293562320844ba87246562a5e2a8325e1718ee4"},
     {file = "simulariumio-1.11.0.tar.gz", hash = "sha256:4f58c25ec633a4f260e78e4ed5c1d89fa12468cf3f3ee2061fe039c83f23c894"},
@@ -4682,6 +4881,7 @@ 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", "bngl", "lems", "neuroml", "simularium"]
 files = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -4693,6 +4893,7 @@ version = "2.73"
 description = "Python package for the Smoldyn simulator"
 optional = false
 python-versions = ">=3.6"
+groups = ["main", "smoldyn"]
 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"},
@@ -4723,6 +4924,7 @@ version = "1.3.1"
 description = "Sniff out which async library your code is running under"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"},
     {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
@@ -4734,6 +4936,7 @@ version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
 optional = false
 python-versions = "*"
+groups = ["docs"]
 files = [
     {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
     {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
@@ -4745,6 +4948,7 @@ version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "docs"]
 files = [
     {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"},
     {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"},
@@ -4756,6 +4960,7 @@ version = "8.0.2"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.10"
+groups = ["docs"]
 files = [
     {file = "sphinx-8.0.2-py3-none-any.whl", hash = "sha256:56173572ae6c1b9a38911786e206a110c9749116745873feae4f9ce88e59391d"},
     {file = "sphinx-8.0.2.tar.gz", hash = "sha256:0cce1ddcc4fd3532cf1dd283bc7d886758362c5c1de6598696579ce96d8ffa5b"},
@@ -4791,6 +4996,7 @@ version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
     {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
@@ -4807,6 +5013,7 @@ version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
     {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
@@ -4823,6 +5030,7 @@ version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
     {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
@@ -4839,6 +5047,7 @@ version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
 optional = false
 python-versions = ">=3.5"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
     {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
@@ -4853,6 +5062,7 @@ version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 files = [
     {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
     {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
@@ -4869,6 +5079,7 @@ version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
 python-versions = ">=3.9"
+groups = ["docs"]
 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"},
@@ -4885,6 +5096,7 @@ version = "0.3.5"
 description = "Decently styled search results for sphinx-doc projects"
 optional = false
 python-versions = "*"
+groups = ["docs"]
 files = []
 develop = false
 
@@ -4900,6 +5112,7 @@ version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 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"},
@@ -4919,6 +5132,7 @@ version = "1.13.3"
 description = "Computer algebra system (CAS) in Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "lems", "neuroml"]
 files = [
     {file = "sympy-1.13.3-py3-none-any.whl", hash = "sha256:54612cf55a62755ee71824ce692986f23c88ffa77207b30c1368eda4a7060f73"},
     {file = "sympy-1.13.3.tar.gz", hash = "sha256:b27fd2c6530e0ab39e275fc9b683895367e51d5da91baa8d3d64db2565fec4d9"},
@@ -4936,6 +5150,7 @@ version = "3.10.1"
 description = "Hierarchical datasets for Python"
 optional = false
 python-versions = ">=3.10"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "tables-3.10.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bca9d11a570ca1bc57f0845e54e55c3093d5a1ace376faee639e09503a73745b"},
     {file = "tables-3.10.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b62881cb682438d1e92b9178db42b160638aef3ca23341f7d98e9b27821b1eb4"},
@@ -4952,6 +5167,10 @@ files = [
     {file = "tables-3.10.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e36ce9f10471c69c1f0b06c6966de762558a35d62592c55df7994a8019adaf0c"},
     {file = "tables-3.10.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f233e78cc9fa4157ec4c3ef2abf01a731fe7969bc6ed73539e5f4cd3b94c98b2"},
     {file = "tables-3.10.1-cp312-cp312-win_amd64.whl", hash = "sha256:34357d2f2f75843a44e6fe54d1f11fc2e35a8fd3cb134df3d3362cff78010adb"},
+    {file = "tables-3.10.1-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:6fc5b46a4f359249c3ab9a0a0a2448d7e680e68cffd63fdf3fb7171781edd46e"},
+    {file = "tables-3.10.1-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:2ecabd7f459d40b7f9f5256850dd5f43773fda7b789f827de92c3d26df1e320f"},
+    {file = "tables-3.10.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:40a4ee18f3c9339d9dd8fd3777c75cda5768f2ff347064a2796f59161a190af8"},
+    {file = "tables-3.10.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:757c6ea257c174af8036cf8f273ede756bbcd6db5ac7e2a4d64e788b0f371152"},
     {file = "tables-3.10.1.tar.gz", hash = "sha256:4aa07ac734b9c037baeaf44aec64ec902ad247f57811b59f30c4e31d31f126cf"},
 ]
 
@@ -4972,6 +5191,7 @@ version = "0.9.0"
 description = "Pretty-print tabular data"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "lems", "neuroml"]
 files = [
     {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"},
     {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"},
@@ -4986,6 +5206,7 @@ version = "2.5.0"
 description = "ANSI color formatting for output in terminal"
 optional = false
 python-versions = ">=3.9"
+groups = ["main"]
 files = [
     {file = "termcolor-2.5.0-py3-none-any.whl", hash = "sha256:37b17b5fc1e604945c2642c872a3764b5d547a48009871aea3edd3afa180afb8"},
     {file = "termcolor-2.5.0.tar.gz", hash = "sha256:998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f"},
@@ -5000,6 +5221,7 @@ version = "0.18.1"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "terminado-0.18.1-py3-none-any.whl", hash = "sha256:a4468e1b37bb318f8a86514f65814e1afc977cf29b3992a4500d9dd305dcceb0"},
     {file = "terminado-0.18.1.tar.gz", hash = "sha256:de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e"},
@@ -5021,6 +5243,7 @@ version = "1.3.0"
 description = "A tiny CSS parser"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "tinycss2-1.3.0-py3-none-any.whl", hash = "sha256:54a8dbdffb334d536851be0226030e9505965bb2f30f21a4a82c55fb2a80fae7"},
     {file = "tinycss2-1.3.0.tar.gz", hash = "sha256:152f9acabd296a8375fbca5b84c961ff95971fcfc32e79550c8df8e29118c54d"},
@@ -5039,6 +5262,8 @@ version = "2.0.2"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "dev", "docs"]
+markers = "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"},
@@ -5046,22 +5271,23 @@ files = [
 
 [[package]]
 name = "tornado"
-version = "6.4.1"
+version = "6.4.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
-    {file = "tornado-6.4.1-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:163b0aafc8e23d8cdc3c9dfb24c5368af84a81e3364745ccb4427669bf84aec8"},
-    {file = "tornado-6.4.1-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:6d5ce3437e18a2b66fbadb183c1d3364fb03f2be71299e7d10dbeeb69f4b2a14"},
-    {file = "tornado-6.4.1-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e2e20b9113cd7293f164dc46fffb13535266e713cdb87bd2d15ddb336e96cfc4"},
-    {file = "tornado-6.4.1-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:8ae50a504a740365267b2a8d1a90c9fbc86b780a39170feca9bcc1787ff80842"},
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-    {file = "tornado-6.4.1-cp38-abi3-win_amd64.whl", hash = "sha256:b24b8982ed444378d7f21d563f4180a2de31ced9d8d84443907a0a64da2072e7"},
-    {file = "tornado-6.4.1.tar.gz", hash = "sha256:92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9"},
+    {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:e828cce1123e9e44ae2a50a9de3055497ab1d0aeb440c5ac23064d9e44880da1"},
+    {file = "tornado-6.4.2-cp38-abi3-macosx_10_9_x86_64.whl", hash = "sha256:072ce12ada169c5b00b7d92a99ba089447ccc993ea2143c9ede887e0937aa803"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1a017d239bd1bb0919f72af256a970624241f070496635784d9bf0db640d3fec"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c36e62ce8f63409301537222faffcef7dfc5284f27eec227389f2ad11b09d946"},
+    {file = "tornado-6.4.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bca9eb02196e789c9cb5c3c7c0f04fb447dc2adffd95265b2c7223a8a615ccbf"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:304463bd0772442ff4d0f5149c6f1c2135a1fae045adf070821c6cdc76980634"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_i686.whl", hash = "sha256:c82c46813ba483a385ab2a99caeaedf92585a1f90defb5693351fa7e4ea0bf73"},
+    {file = "tornado-6.4.2-cp38-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:932d195ca9015956fa502c6b56af9eb06106140d844a335590c1ec7f5277d10c"},
+    {file = "tornado-6.4.2-cp38-abi3-win32.whl", hash = "sha256:2876cef82e6c5978fde1e0d5b1f919d756968d5b4282418f3146b79b58556482"},
+    {file = "tornado-6.4.2-cp38-abi3-win_amd64.whl", hash = "sha256:908b71bf3ff37d81073356a5fadcc660eb10c1476ee6e2725588626ce7e5ca38"},
+    {file = "tornado-6.4.2.tar.gz", hash = "sha256:92bad5b4746e9879fd7bf1eb21dce4e3fc5128d71601f80005afa39237ad620b"},
 ]
 
 [[package]]
@@ -5070,6 +5296,7 @@ version = "5.14.3"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
     {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
@@ -5085,6 +5312,7 @@ version = "2.9.0.20241003"
 description = "Typing stubs for python-dateutil"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "types-python-dateutil-2.9.0.20241003.tar.gz", hash = "sha256:58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446"},
     {file = "types_python_dateutil-2.9.0.20241003-py3-none-any.whl", hash = "sha256:250e1d8e80e7bbc3a6c99b907762711d1a1cdd00e978ad39cb5940f6f0a87f3d"},
@@ -5096,10 +5324,12 @@ version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "docs", "lems", "neuroml", "simularium"]
 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"},
 ]
+markers = {bngl = "python_version <= \"3.11\""}
 
 [[package]]
 name = "tzdata"
@@ -5107,6 +5337,7 @@ version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
+groups = ["main", "bngl", "simularium"]
 files = [
     {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
     {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
@@ -5118,6 +5349,7 @@ version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
 optional = false
 python-versions = ">=3.7"
+groups = ["main", "bngl"]
 files = [
     {file = "uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7"},
     {file = "uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363"},
@@ -5132,6 +5364,7 @@ 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"},
@@ -5143,13 +5376,14 @@ version = "2.2.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl", "containers", "dev", "docs"]
 files = [
     {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"},
     {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"},
 ]
 
 [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)"]
@@ -5160,6 +5394,7 @@ version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
     {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
@@ -5171,6 +5406,7 @@ version = "24.8.0"
 description = "A library for working with the color formats defined by HTML and CSS."
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "webcolors-24.8.0-py3-none-any.whl", hash = "sha256:fc4c3b59358ada164552084a8ebee637c221e4059267d0f8325b3b560f6c7f0a"},
     {file = "webcolors-24.8.0.tar.gz", hash = "sha256:08b07af286a01bcd30d583a7acadf629583d1f79bfef27dd2c2c5c263817277d"},
@@ -5186,6 +5422,7 @@ version = "0.5.1"
 description = "Character encoding aliases for legacy web content"
 optional = false
 python-versions = "*"
+groups = ["main", "bngl"]
 files = [
     {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"},
     {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
@@ -5197,6 +5434,7 @@ version = "1.8.0"
 description = "WebSocket client for Python with low level API options"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "bngl"]
 files = [
     {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"},
     {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"},
@@ -5213,6 +5451,7 @@ version = "0.14.0"
 description = "Makes working with XML feel like you are working with JSON"
 optional = false
 python-versions = ">=3.4"
+groups = ["main", "bngl"]
 files = [
     {file = "xmltodict-0.14.0-py2.py3-none-any.whl", hash = "sha256:6dd20b8de8d0eb84d175ec706cc17b53df236615b0980de33537736319e5ee85"},
     {file = "xmltodict-0.14.0.tar.gz", hash = "sha256:8b39b25b564fd466be566c9e8a869cc4b5083c2fec7f98665f47bf0853f6cc77"},
@@ -5224,6 +5463,7 @@ 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"},
@@ -5246,6 +5486,6 @@ simularium = ["simulariumio"]
 smoldyn = ["smoldyn"]
 
 [metadata]
-lock-version = "2.0"
+lock-version = "2.1"
 python-versions = "^3.10"
 content-hash = "30ee3f3b6158a01484ab2ae1b32ba5b8c93ffb652baf60c015e380e6a91cad9a"