From fe9649d97aa83fa0a3a422a01f8e265c130608a8 Mon Sep 17 00:00:00 2001
From: "Pablo R. Mier" <pablo.rodriguez.mier@gmail.com>
Date: Wed, 24 Apr 2024 21:02:48 +0200
Subject: [PATCH] Update lock and fix networkx dep

---
 poetry.lock    | 1692 ++++++++++++++++++++++++++++++------------------
 pyproject.toml |    2 +-
 2 files changed, 1078 insertions(+), 616 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 014d0026..b6ba96db 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -25,6 +25,33 @@ files = [
     {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
+[[package]]
+name = "anndata"
+version = "0.10.7"
+description = "Annotated data."
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "anndata-0.10.7-py3-none-any.whl", hash = "sha256:8b50af790f9a73414d0b94fd7b8e005f5cc6c53c33eb09206d2bd6720115bffc"},
+    {file = "anndata-0.10.7.tar.gz", hash = "sha256:9b186bea18956fefdc35e7464d822a17e9faa456ca2d20c7a0966a4837b822a2"},
+]
+
+[package.dependencies]
+array-api-compat = ">1.4,<1.5 || >1.5"
+exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
+h5py = ">=3.1"
+natsort = "*"
+numpy = ">=1.23"
+packaging = ">=20.0"
+pandas = ">=1.4,<2.1.0rc0 || >2.1.0rc0,<2.1.2 || >2.1.2"
+scipy = ">1.8"
+
+[package.extras]
+dev = ["pytest-xdist", "setuptools-scm"]
+doc = ["awkward (>=2.0.7)", "ipython", "myst-parser", "nbsphinx", "readthedocs-sphinx-search", "scanpydoc[theme,typehints] (>=0.13.4)", "sphinx (>=4.4)", "sphinx-autodoc-typehints (>=1.11.0)", "sphinx-book-theme (>=1.1.0)", "sphinx-copybutton", "sphinx-design (>=0.5.0)", "sphinx-issues", "sphinxext-opengraph", "zarr"]
+gpu = ["cupy"]
+test = ["awkward (>=2.3)", "boltons", "dask[array,distributed] (>=2022.09.2)", "httpx", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pyarrow", "pytest (>=7.3)", "pytest-cov (>=2.10)", "pytest-memray", "pytest-mock", "scanpy", "scikit-learn", "zarr"]
+
 [[package]]
 name = "annotated-types"
 version = "0.6.0"
@@ -80,6 +107,24 @@ files = [
     {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
 ]
 
+[[package]]
+name = "array-api-compat"
+version = "1.6"
+description = "A wrapper around NumPy and other array libraries to make them compatible with the Array API standard"
+optional = true
+python-versions = "*"
+files = [
+    {file = "array_api_compat-1.6-py3-none-any.whl", hash = "sha256:0f132e698952bcebccfa941b4fc02cbc754802474b13a564208cf6cdbffb51e1"},
+    {file = "array_api_compat-1.6.tar.gz", hash = "sha256:74a1e355cdabb9cf6c48922a5d07976d9230025d65731bef17174151b64876af"},
+]
+
+[package.extras]
+cupy = ["cupy"]
+dask = ["dask"]
+jax = ["jax"]
+numpy = ["numpy"]
+pytorch = ["pytorch"]
+
 [[package]]
 name = "asttokens"
 version = "2.4.1"
@@ -451,13 +496,13 @@ files = [
 
 [[package]]
 name = "comm"
-version = "0.2.1"
+version = "0.2.2"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "comm-0.2.1-py3-none-any.whl", hash = "sha256:87928485c0dfc0e7976fd89fc1e187023cf587e7c353e4a9b417555b44adf021"},
-    {file = "comm-0.2.1.tar.gz", hash = "sha256:0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a"},
+    {file = "comm-0.2.2-py3-none-any.whl", hash = "sha256:e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3"},
+    {file = "comm-0.2.2.tar.gz", hash = "sha256:3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e"},
 ]
 
 [package.dependencies]
@@ -468,64 +513,64 @@ test = ["pytest"]
 
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 name = "contourpy"
-version = "1.2.0"
+version = "1.2.1"
 description = "Python library for calculating contours of 2D quadrilateral grids"
 optional = false
 python-versions = ">=3.9"
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 [package.extras]
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 docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
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 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
 test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
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 docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
 tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
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+version = "0.91.6"
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+optional = true
+python-versions = "*"
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+
+[package.dependencies]
+numpy = ">=1.5.0"
+scipy = ">=0.10.0"
+
 [[package]]
 name = "debugpy"
 version = "1.8.1"
@@ -676,6 +764,23 @@ files = [
     {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
 ]
 
+[[package]]
+name = "decoupler"
+version = "1.6.0"
+description = "Ensemble of methods to infer biological activities from omics data"
+optional = true
+python-versions = ">=3.6"
+files = [
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+]
+
+[package.dependencies]
+anndata = "*"
+numba = "*"
+tqdm = "*"
+typing-extensions = "*"
+
 [[package]]
 name = "depinfo"
 version = "2.2.0"
@@ -702,6 +807,19 @@ files = [
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 ]
 
+[[package]]
+name = "docrep"
+version = "0.3.2"
+description = "Python package for docstring repetition"
+optional = true
+python-versions = "*"
+files = [
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+]
+
+[package.dependencies]
+six = "*"
+
 [[package]]
 name = "docutils"
 version = "0.19"
@@ -747,13 +865,13 @@ scipy = ">=0.9"
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.0"
+version = "1.2.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -787,55 +905,71 @@ files = [
 [package.extras]
 devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
 
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+description = "the modular source code checker: pep8 pyflakes and co"
+optional = false
+python-versions = ">=3.8.1"
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+pycodestyle = ">=2.11.0,<2.12.0"
+pyflakes = ">=3.2.0,<3.3.0"
+
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 ]
 
 [package.extras]
@@ -865,19 +999,19 @@ files = [
 
 [[package]]
 name = "graphviz"
-version = "0.20.1"
+version = "0.20.3"
 description = "Simple Python interface for Graphviz"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
 dev = ["flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"]
-docs = ["sphinx (>=5)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
-test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=3)"]
+docs = ["sphinx (>=5,<7)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
+test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
 
 [[package]]
 name = "greenlet"
@@ -993,15 +1127,48 @@ files = [
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 ]
 
+[[package]]
+name = "h5py"
+version = "3.11.0"
+description = "Read and write HDF5 files from Python"
+optional = true
+python-versions = ">=3.8"
+files = [
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+    {file = "h5py-3.11.0.tar.gz", hash = "sha256:7b7e8f78072a2edec87c9836f25f34203fd492a4475709a18b417a33cfb21fa9"},
+]
+
+[package.dependencies]
+numpy = ">=1.17.3"
+
 [[package]]
 name = "httpcore"
-version = "1.0.4"
+version = "1.0.5"
 description = "A minimal low-level HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpcore-1.0.4-py3-none-any.whl", hash = "sha256:ac418c1db41bade2ad53ae2f3834a3a0f5ae76b56cf5aa497d2d033384fc7d73"},
-    {file = "httpcore-1.0.4.tar.gz", hash = "sha256:cb2839ccfcba0d2d3c1131d3c3e26dfc327326fbe7a5dc0dbfe9f6c9151bb022"},
+    {file = "httpcore-1.0.5-py3-none-any.whl", hash = "sha256:421f18bac248b25d310f3cacd198d55b8e6125c107797b609ff9b7a6ba7991b5"},
+    {file = "httpcore-1.0.5.tar.gz", hash = "sha256:34a38e2f9291467ee3b44e89dd52615370e152954ba21721378a87b2960f7a61"},
 ]
 
 [package.dependencies]
@@ -1012,7 +1179,7 @@ h11 = ">=0.13,<0.15"
 asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
-trio = ["trio (>=0.22.0,<0.25.0)"]
+trio = ["trio (>=0.22.0,<0.26.0)"]
 
 [[package]]
 name = "httpx"
@@ -1040,13 +1207,13 @@ socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "idna"
-version = "3.6"
+version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
-    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
+    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
+    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
 ]
 
 [[package]]
@@ -1062,13 +1229,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.0.2"
+version = "7.1.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-7.0.2-py3-none-any.whl", hash = "sha256:f4bc4c0c070c490abf4ce96d715f68e95923320370efb66143df00199bb6c100"},
-    {file = "importlib_metadata-7.0.2.tar.gz", hash = "sha256:198f568f3230878cb1b44fbd7975f87906c22336dba2e4a7f05278c281fbd792"},
+    {file = "importlib_metadata-7.1.0-py3-none-any.whl", hash = "sha256:30962b96c0c223483ed6cc7280e7f0199feb01a0e40cfae4d4450fc6fab1f570"},
+    {file = "importlib_metadata-7.1.0.tar.gz", hash = "sha256:b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2"},
 ]
 
 [package.dependencies]
@@ -1077,17 +1244,17 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.3"
+version = "6.4.0"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.3-py3-none-any.whl", hash = "sha256:4c0269e3580fe2634d364b39b38b961540a7738c02cb984e98add8b4221d793d"},
-    {file = "importlib_resources-6.1.3.tar.gz", hash = "sha256:56fb4525197b78544a3354ea27793952ab93f935bb4bf746b846bb1015020f2b"},
+    {file = "importlib_resources-6.4.0-py3-none-any.whl", hash = "sha256:50d10f043df931902d4194ea07ec57960f66a80449ff867bfe782b4c486ba78c"},
+    {file = "importlib_resources-6.4.0.tar.gz", hash = "sha256:cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145"},
 ]
 
 [package.dependencies]
@@ -1095,7 +1262,27 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["jaraco.collections", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
+testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
+
+[[package]]
+name = "inflect"
+version = "7.2.1"
+description = "Correctly generate plurals, singular nouns, ordinals, indefinite articles"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "inflect-7.2.1-py3-none-any.whl", hash = "sha256:f4ecaffaeccbc746251d973c0674c47d63b262fdad63f651fb98e878eee1f449"},
+    {file = "inflect-7.2.1.tar.gz", hash = "sha256:a7ce5e23d6798734f256c1ad9ed52186b8ec276f10b18ce3d3ecb19c21eb6cb6"},
+]
+
+[package.dependencies]
+more-itertools = "*"
+typeguard = ">=4.0.1"
+typing-extensions = "*"
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["pygments", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "iniconfig"
@@ -1110,13 +1297,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.29.3"
+version = "6.29.4"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.29.3-py3-none-any.whl", hash = "sha256:5aa086a4175b0229d4eca211e181fb473ea78ffd9869af36ba7694c947302a21"},
-    {file = "ipykernel-6.29.3.tar.gz", hash = "sha256:e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2"},
+    {file = "ipykernel-6.29.4-py3-none-any.whl", hash = "sha256:1181e653d95c6808039c509ef8e67c4126b3b3af7781496c7cbfb5ed938a27da"},
+    {file = "ipykernel-6.29.4.tar.gz", hash = "sha256:3d44070060f9475ac2092b760123fadf105d2e2493c24848b6691a7c4f42af5c"},
 ]
 
 [package.dependencies]
@@ -1278,13 +1465,13 @@ testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbforma
 
 [[package]]
 name = "jupyter-client"
-version = "8.6.0"
+version = "8.6.1"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-8.6.0-py3-none-any.whl", hash = "sha256:909c474dbe62582ae62b758bca86d6518c85234bdee2d908c778db6d72f39d99"},
-    {file = "jupyter_client-8.6.0.tar.gz", hash = "sha256:0642244bb83b4764ae60d07e010e15f0e2d275ec4e918a8f7b80fbbef3ca60c7"},
+    {file = "jupyter_client-8.6.1-py3-none-any.whl", hash = "sha256:3b7bd22f058434e3b9a7ea4b1500ed47de2713872288c0d511d19926f99b459f"},
+    {file = "jupyter_client-8.6.1.tar.gz", hash = "sha256:e842515e2bab8e19186d89fdfea7abd15e39dd581f94e399f00e2af5a1652d3f"},
 ]
 
 [package.dependencies]
@@ -1301,13 +1488,13 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 
 [[package]]
 name = "jupyter-core"
-version = "5.7.1"
+version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_core-5.7.1-py3-none-any.whl", hash = "sha256:c65c82126453a723a2804aa52409930434598fd9d35091d63dfb919d2b765bb7"},
-    {file = "jupyter_core-5.7.1.tar.gz", hash = "sha256:de61a9d7fc71240f688b2fb5ab659fbb56979458dc66a71decd098e03c79e218"},
+    {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"},
+    {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"},
 ]
 
 [package.dependencies]
@@ -1317,7 +1504,7 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
-test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "kiwisolver"
@@ -1443,6 +1630,36 @@ files = [
     {file = "latexcodec-3.0.0.tar.gz", hash = "sha256:917dc5fe242762cc19d963e6548b42d63a118028cdd3361d62397e3b638b6bc5"},
 ]
 
+[[package]]
+name = "llvmlite"
+version = "0.42.0"
+description = "lightweight wrapper around basic LLVM functionality"
+optional = true
+python-versions = ">=3.9"
+files = [
+    {file = "llvmlite-0.42.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:3366938e1bf63d26c34fbfb4c8e8d2ded57d11e0567d5bb243d89aab1eb56098"},
+    {file = "llvmlite-0.42.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c35da49666a21185d21b551fc3caf46a935d54d66969d32d72af109b5e7d2b6f"},
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 ]
 
 [package.dependencies]
@@ -1579,7 +1796,7 @@ cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
 kiwisolver = ">=1.3.1"
-numpy = ">=1.21,<2"
+numpy = ">=1.21"
 packaging = ">=20.0"
 pillow = ">=8"
 pyparsing = ">=2.3.1"
@@ -1587,18 +1804,29 @@ python-dateutil = ">=2.7"
 
 [[package]]
 name = "matplotlib-inline"
-version = "0.1.6"
+version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 traitlets = "*"
 
+[[package]]
+name = "mccabe"
+version = "0.7.0"
+description = "McCabe checker, plugin for flake8"
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
 [[package]]
 name = "mdit-py-plugins"
 version = "0.3.5"
@@ -1629,6 +1857,17 @@ files = [
     {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
 ]
 
+[[package]]
+name = "more-itertools"
+version = "10.2.0"
+description = "More routines for operating on iterables, beyond itertools"
+optional = true
+python-versions = ">=3.8"
+files = [
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+]
+
 [[package]]
 name = "mpmath"
 version = "1.3.0"
@@ -1711,6 +1950,21 @@ linkify = ["linkify-it-py (>=1.0,<2.0)"]
 rtd = ["ipython", "sphinx-book-theme", "sphinx-design", "sphinxcontrib.mermaid (>=0.7.1,<0.8.0)", "sphinxext-opengraph (>=0.6.3,<0.7.0)", "sphinxext-rediraffe (>=0.2.7,<0.3.0)"]
 testing = ["beautifulsoup4", "coverage[toml]", "pytest (>=6,<7)", "pytest-cov", "pytest-param-files (>=0.3.4,<0.4.0)", "pytest-regressions", "sphinx (<5.2)", "sphinx-pytest"]
 
+[[package]]
+name = "natsort"
+version = "8.4.0"
+description = "Simple yet flexible natural sorting in Python."
+optional = true
+python-versions = ">=3.7"
+files = [
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+icu = ["PyICU (>=1.0.0)"]
+
 [[package]]
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 version = "0.7.4"
@@ -1735,19 +1989,19 @@ test = ["flaky", "ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "p
 
 [[package]]
 name = "nbformat"
-version = "5.9.2"
+version = "5.10.4"
 description = "The Jupyter Notebook format"
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 [package.dependencies]
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-jupyter-core = "*"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 traitlets = ">=5.1"
 
 [package.extras]
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 test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
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+version = "0.59.1"
+description = "compiling Python code using LLVM"
+optional = true
+python-versions = ">=3.9"
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+numpy = ">=1.22,<1.27"
+
 [[package]]
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 version = "1.26.4"
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+optional = true
+python-versions = ">=3.7"
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+wrapt = ">=1.12.0"
+
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+graph = ["networkx (>=2.3.0)"]
+tests = ["tox (>=3.20.1)"]
+
 [[package]]
 name = "optlang"
 version = "1.8.1"
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 [package.dependencies]
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-    {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
-    {version = ">=1.26.0,<2", markers = "python_version >= \"3.12\""},
+    {version = ">=1.22.4", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2", markers = "python_version == \"3.11\""},
+    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
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 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1976,18 +2293,18 @@ xml = ["lxml (>=4.9.2)"]
 
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-version = "0.8.3"
+version = "0.8.4"
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+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+testing = ["docopt", "pytest"]
 
 [[package]]
 name = "pathspec"
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 [package.extras]
@@ -2115,28 +2433,29 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.2.1"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
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 test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+type = ["mypy (>=1.8)"]
 
 [[package]]
 name = "pluggy"
-version = "1.4.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2226,17 +2545,17 @@ tests = ["pytest"]
 
 [[package]]
 name = "pybind11"
-version = "2.11.1"
+version = "2.12.0"
 description = "Seamless operability between C++11 and Python"
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.extras]
-global = ["pybind11-global (==2.11.1)"]
+global = ["pybind11-global (==2.12.0)"]
 
 [[package]]
 name = "pybtex"
@@ -2272,31 +2591,42 @@ files = [
 docutils = ">=0.14"
 pybtex = ">=0.16"
 
+[[package]]
+name = "pycodestyle"
+version = "2.11.1"
+description = "Python style guide checker"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
 [[package]]
 name = "pycparser"
-version = "2.21"
+version = "2.22"
 description = "C parser in Python"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "pydantic"
-version = "2.6.3"
+version = "2.7.1"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 annotated-types = ">=0.4.0"
-pydantic-core = "2.16.3"
+pydantic-core = "2.18.2"
 typing-extensions = ">=4.6.1"
 
 [package.extras]
@@ -2304,90 +2634,90 @@ email = ["email-validator (>=2.0.0)"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.16.3"
-description = ""
+version = "2.18.2"
+description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.8"
 files = [
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 test = ["pytest", "pytest-cov", "pytest-regressions"]
 
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 version = "2.17.2"
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 [[package]]
 name = "scs"
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+
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 python-versions = ">=3.8"
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 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [extras]
-default = ["cvxpy", "gurobipy", "scipy"]
+cvxpy = ["cvxpy"]
+gurobi = ["cvxpy", "gurobipy"]
+matplotlib = ["matplotlib"]
+networkx = ["networkx"]
 os = ["cvxpy", "pyscipopt", "scipy"]
+picos = ["PICOS"]
+recommended = ["cvxpy", "gurobipy", "matplotlib", "scipy"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9 <4"
-content-hash = "e106650a34464040485d78a5874c48b7a87d092a5a22f60645749984f65861d6"
+content-hash = "59689dadcf01dd8f0ae27db82d7ae7d0fca0a21c7879d931137ae554e9c6a83a"
diff --git a/pyproject.toml b/pyproject.toml
index 70329c16..698d103a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,7 @@ scipy = {version = "^1.13.0", optional = true}
 pyscipopt = {version = "^5.0.0", optional = true}
 gurobipy = {version = "^11.0.1",  optional = true}
 # Contrib
-networkx = {version = "^3.3", optional = true}
+networkx = {version = ">=3.0", optional = true}
 omnipath = {version = "^1.0.8", optional = true}
 decoupler = {version = "^1.6.0", optional = true}
 cobra = {version = "^0.29.0", optional = true}