From 18b8fdfef20b03888ab486ba15592e45d61f29f5 Mon Sep 17 00:00:00 2001
From: Gensollen <nicolas.gensollen@gmail.com>
Date: Fri, 27 Sep 2024 19:58:35 +0200
Subject: [PATCH] [FIX] Bump scipy and make brainstat optional (#1304)

---
 poetry.lock    | 1454 ++++++++++++++++++++++++++----------------------
 pyproject.toml |    7 +-
 2 files changed, 784 insertions(+), 677 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a950eeba6..e9cfd6a1f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -172,13 +172,13 @@ bidsschematools = ">=0.10"
 
 [[package]]
 name = "bidsschematools"
-version = "0.11.0"
+version = "0.11.3"
 description = "Python tools for working with the BIDS schema."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "bidsschematools-0.11.0-py3-none-any.whl", hash = "sha256:2cd8425860a683facc3db50692133d1ea619a4e61b635fae0aa8f00c2587fe67"},
-    {file = "bidsschematools-0.11.0.tar.gz", hash = "sha256:ba9b8406face17782f0aa5a48a84c4a161dc3497f498edae97c7c49d637ab71f"},
+    {file = "bidsschematools-0.11.3-py3-none-any.whl", hash = "sha256:94ac739b01c66b5771e13ea9c3575f60b6d860f8f5da3e42d93ec81bcbf10941"},
+    {file = "bidsschematools-0.11.3.tar.gz", hash = "sha256:1af477a4e5d799da631f6c5d2feb6b84b5ba65db13a4459474d525550e20157a"},
 ]
 
 [package.dependencies]
@@ -256,13 +256,13 @@ test = ["coverage", "coveralls", "matplotlib (>=2.0.0)", "nibabel", "numpy (>=1.
 
 [[package]]
 name = "brainstat"
-version = "0.3.6"
+version = "0.4.2"
 description = "A toolbox for statistical analysis of neuroimaging data"
 optional = false
 python-versions = ">=3.7.*"
 files = [
-    {file = "brainstat-0.3.6-py3-none-any.whl", hash = "sha256:47e266120c88a1d305221bacf703462575eea49749943bd96340a5be8b340701"},
-    {file = "brainstat-0.3.6.tar.gz", hash = "sha256:de39767f3c21a8312434e8df66f3f7b98c82fb455e8ae0c90fb7b968c13e7a7e"},
+    {file = "brainstat-0.4.2-py3-none-any.whl", hash = "sha256:4a2a1f18febdfbd25e1b9ebbcf21b8bf9c71884181bf3f31adf7be45ff299927"},
+    {file = "brainstat-0.4.2.tar.gz", hash = "sha256:798c9ba4888259aacd1d6d86782d7b94075e23f86c2103ae5b66b26698c3e814"},
 ]
 
 [package.dependencies]
@@ -286,13 +286,13 @@ dev = ["gitpython", "hcp-utils", "mypy", "plotly", "pytest"]
 
 [[package]]
 name = "cattrs"
-version = "23.2.3"
+version = "24.1.2"
 description = "Composable complex class support for attrs and dataclasses."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "cattrs-23.2.3-py3-none-any.whl", hash = "sha256:0341994d94971052e9ee70662542699a3162ea1e0c62f7ce1b4a57f563685108"},
-    {file = "cattrs-23.2.3.tar.gz", hash = "sha256:a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f"},
+    {file = "cattrs-24.1.2-py3-none-any.whl", hash = "sha256:67c7495b760168d931a10233f979b28dc04daf853b30752246f4f8471c6d68d0"},
+    {file = "cattrs-24.1.2.tar.gz", hash = "sha256:8028cfe1ff5382df59dd36474a86e02d817b06eaf8af84555441bac915d2ef85"},
 ]
 
 [package.dependencies]
@@ -304,6 +304,7 @@ 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)"]
 pyyaml = ["pyyaml (>=6.0)"]
 tomlkit = ["tomlkit (>=0.11.8)"]
@@ -311,13 +312,13 @@ ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
-version = "2024.7.4"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
-    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
@@ -538,66 +539,87 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 
 [[package]]
 name = "contourpy"
-version = "1.2.1"
+version = "1.3.0"
 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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+test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
@@ -772,69 +794,75 @@ testing = ["hatch", "pre-commit", "pytest", "tox"]
 
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 [package.extras]
@@ -1018,48 +1061,56 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "h5py"
-version = "3.11.0"
+version = "3.12.1"
 description = "Read and write HDF5 files from Python"
 optional = false
-python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
-numpy = ">=1.17.3"
+numpy = ">=1.19.3"
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "imageio"
 version = "2.35.1"
@@ -1095,32 +1146,36 @@ tifffile = ["tifffile"]
 
 [[package]]
 name = "importlib-metadata"
-version = "8.4.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
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+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.4.4"
+version = "6.4.5"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1312,115 +1367,125 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "kiwisolver"
-version = "1.4.5"
+version = "1.4.7"
 description = "A fast implementation of the Cassowary constraint solver"
 optional = false
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+python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -2428,29 +2512,29 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.2"
+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"
 files = [
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 ]
 
 [package.extras]
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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)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "plotly"
-version = "5.23.0"
+version = "5.24.1"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2552,13 +2636,13 @@ docs = ["matplotlib", "numpy", "numpydoc", "pillow", "sphinx", "sphinx-copybutto
 
 [[package]]
 name = "pydot"
-version = "3.0.1"
+version = "3.0.2"
 description = "Python interface to Graphviz's Dot"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pydot-3.0.2.tar.gz", hash = "sha256:9180da540b51b3aa09fbf81140b3edfbe2315d778e8589a7d0a4a69c41332bae"},
 ]
 
 [package.dependencies]
@@ -2567,7 +2651,7 @@ pyparsing = ">=3.0.9"
 [package.extras]
 dev = ["chardet", "parameterized", "ruff"]
 release = ["zest.releaser[recommended]"]
-tests = ["chardet", "parameterized", "ruff", "tox", "unittest-parallel"]
+tests = ["chardet", "parameterized", "pytest", "pytest-cov", "pytest-xdist[psutil]", "ruff", "tox"]
 
 [[package]]
 name = "pydra"
@@ -2714,13 +2798,13 @@ tests = ["codecov", "coverage", "coveralls", "flake8", "flake8-black", "flake8-d
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.9"
+version = "10.10.2"
 description = "Extension pack for Python Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2732,13 +2816,13 @@ extra = ["pygments (>=2.12)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.2"
+version = "3.1.4"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
 files = [
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 ]
 
 [package.extras]
@@ -2746,13 +2830,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "8.3.2"
+version = "8.3.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2865,13 +2949,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -2988,90 +3072,105 @@ rpds-py = ">=0.7.0"
 
 [[package]]
 name = "regex"
-version = "2024.7.24"
+version = "2024.9.11"
 description = "Alternative regular expression module, to replace re."
 optional = false
 python-versions = ">=3.8"
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 [[package]]
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 [[package]]
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 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
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 [package.dependencies]
@@ -3326,11 +3425,11 @@ threadpoolctl = ">=3.1.0"
 [package.extras]
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 ]
 
 [package.dependencies]
-numpy = ">=1.22.3"
+numpy = ">=1.22.3,<3"
 packaging = ">=21.3"
 pandas = ">=1.4,<2.1.0 || >2.1.0"
 patsy = ">=0.5.6"
 scipy = ">=1.8,<1.9.2 || >1.9.2"
 
 [package.extras]
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-develop = ["colorama", "cython (>=0.29.33)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=8.0,<9.0)"]
+build = ["cython (>=3.0.10)"]
+develop = ["colorama", "cython (>=3.0.10)", "cython (>=3.0.10,<4)", "flake8", "isort", "joblib", "matplotlib (>=3)", "pytest (>=7.3.0,<8)", "pytest-cov", "pytest-randomly", "pytest-xdist", "pywinpty", "setuptools-scm[toml] (>=8.0,<9.0)"]
 docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "numpydoc", "pandas-datareader", "sphinx"]
 
 [[package]]
 name = "sympy"
-version = "1.13.2"
+version = "1.13.3"
 description = "Computer algebra system (CAS) in Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3676,13 +3781,13 @@ dev = ["hypothesis (>=6.70.0)", "pytest (>=7.1.0)"]
 
 [[package]]
 name = "templateflow"
-version = "24.2.0"
+version = "24.2.2"
 description = "TemplateFlow Python Client - TemplateFlow is the Zone of neuroimaging templates."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3692,12 +3797,12 @@ requests = "*"
 tqdm = "*"
 
 [package.extras]
-all = ["templateflow[datalad,doc,test]"]
-datalad = ["datalad (>=0.19.0,<0.20.0)"]
+all = ["coverage (>=5.0.0,<5.1.0)", "datalad (>=1.0.0,<1.1.0)", "nbsphinx", "packaging", "pydot (>=1.2.3)", "pydotplus", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "sphinx (>=4.0,<5.0)", "sphinx-click", "sphinx-multiversion", "sphinx-rtd-theme (>=0.4.3)", "sphinxcontrib-apidoc", "toml"]
+datalad = ["datalad (>=1.0.0,<1.1.0)"]
 doc = ["nbsphinx", "packaging", "pydot (>=1.2.3)", "pydotplus", "sphinx (>=4.0,<5.0)", "sphinx-click", "sphinx-multiversion", "sphinx-rtd-theme (>=0.4.3)", "sphinxcontrib-apidoc"]
-docs = ["templateflow[doc]"]
-test = ["coverage", "pytest", "pytest-cov (==2.5.1)", "pytest-xdist"]
-tests = ["templateflow[test]"]
+docs = ["nbsphinx", "packaging", "pydot (>=1.2.3)", "pydotplus", "sphinx (>=4.0,<5.0)", "sphinx-click", "sphinx-multiversion", "sphinx-rtd-theme (>=0.4.3)", "sphinxcontrib-apidoc"]
+test = ["coverage (>=5.0.0,<5.1.0)", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "toml"]
+tests = ["coverage (>=5.0.0,<5.1.0)", "pytest", "pytest-cov", "pytest-env", "pytest-xdist", "toml"]
 
 [[package]]
 name = "tenacity"
@@ -3727,13 +3832,13 @@ files = [
 
 [[package]]
 name = "tifffile"
-version = "2024.8.10"
+version = "2024.8.30"
 description = "Read and write TIFF files"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -3828,13 +3933,13 @@ test = ["Cython", "PySide2", "Sphinx (>=2.1.0,!=3.2.0)", "flake8", "flake8-ets",
 
 [[package]]
 name = "trimesh"
-version = "4.4.7"
+version = "4.4.9"
 description = "Import, export, process, analyze and view triangular meshes."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3844,7 +3949,7 @@ numpy = ">=1.20"
 all = ["trimesh[deprecated,easy,recommend,test]"]
 deprecated = ["gmsh (==4.12.2)"]
 easy = ["chardet", "colorlog", "embreex", "httpx", "jsonschema", "lxml", "manifold3d (>=2.3.0)", "mapbox-earcut (>=1.0.2)", "networkx", "pillow", "pycollada", "rtree", "scipy", "setuptools", "shapely", "svg.path", "vhacdx", "xatlas", "xxhash"]
-recommend = ["cascadio", "glooey", "meshio", "openctm", "psutil", "pyglet (<2)", "python-fcl", "scikit-image", "sympy"]
+recommend = ["cascadio", "fast-simplification", "glooey", "meshio", "openctm", "psutil", "pyglet (<2)", "scikit-image", "sympy"]
 test = ["coveralls", "ezdxf", "matplotlib", "pyinstrument", "pymeshlab", "pyright", "pytest", "pytest-beartype", "pytest-cov", "ruff"]
 
 [[package]]
@@ -3860,24 +3965,24 @@ files = [
 
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
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-    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
+    {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.2.2"
+version = "2.2.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
+    {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"},
+    {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"},
 ]
 
 [package.extras]
@@ -3929,46 +4034,41 @@ web = ["wslink (>=1.0.4)"]
 
 [[package]]
 name = "watchdog"
-version = "4.0.2"
+version = "5.0.2"
 description = "Filesystem events monitoring"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "watchdog-5.0.2-py3-none-win_amd64.whl", hash = "sha256:d010be060c996db725fbce7e3ef14687cdcc76f4ca0e4339a68cc4532c382a73"},
+    {file = "watchdog-5.0.2-py3-none-win_ia64.whl", hash = "sha256:3960136b2b619510569b90f0cd96408591d6c251a75c97690f4553ca88889769"},
+    {file = "watchdog-5.0.2.tar.gz", hash = "sha256:dcebf7e475001d2cdeb020be630dc5b687e9acdd60d16fea6bb4508e7b94cf76"},
 ]
 
 [package.extras]
@@ -4126,20 +4226,24 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.20.0"
+version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
-    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
+    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "3c70832d04eea028d5eff1b9f4219beef752bfd71a19916009dcfeb409584042"
+content-hash = "4942e35961f03324d5315da42cda1b253023426bf395c2de715e0983515f73ba"
diff --git a/pyproject.toml b/pyproject.toml
index 51a4af2db..5cc786de6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,7 @@ scikit-learn = "^1.0"
 nilearn = "^0.10.3"
 colorlog = "^5"
 xgboost = "*"
-scipy = "^1.7"
+scipy = "^1.12"
 matplotlib = "*"
 scikit-image = "*"
 pydicom = "*"
@@ -55,7 +55,6 @@ pybids = "^0.16"
 joblib = "^1.2.0"
 attrs = ">=20.1.0"
 cattrs = "*"
-brainstat = "^0.3.6"
 pydra-bids = "^0.0.10"
 pydra-freesurfer = "^0.0.9"
 pydra-petpvc="^0.0.4"
@@ -79,6 +78,10 @@ mkdocs = "^1.1"
 mkdocs-material = ">=7.1.8"
 pymdown-extensions = "*"
 
+
+[tool.poetry.group.optional.dependencies]
+brainstat = "^0.4.2"
+
 [tool.poetry.scripts]
 clinica = "clinica.cmdline:main"