conda-env.yml

@@ -3,23 +3,23 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.10
+  - python>=3.10,<=3.11
   - click=8.1.*
-  - numpy>=1.22,<1.24
-  - pandas>=1.4.0,<1.6
-  - nibabel>=3.2.0,<4.1
-  - nilearn>=0.9.0,<=0.10.0
-  - sqlalchemy>=1.4.27,<= 1.5.0
+  - numpy>=1.22,<1.27
+  - pandas>=1.4.0,<2.2
+  - nibabel>=3.2.0,<5.2
+  - nilearn>=0.9.0,<=0.10.1
+  - sqlalchemy>=1.4.27,<= 2.0.21
   - ruamel.yaml=0.17.*
-  - h5py=3.8.*
-  - seaborn=0.11.*
-  - Sphinx=5.3.*
-  - sphinx-gallery=0.11.*
-  - furo>=2022.9.29,<2023.0.0
-  - numpydoc=1.5.*
-  - sphinx-copybutton=0.5.*
-  - towncrier=22.12.*
-  - sphinxcontrib-mermaid=0.8.*
+  - h5py>=3.8,<=3.9
+  - seaborn>=0.11,<=0.13
+  - sphinx>=5.3,<7.3
+  - sphinx-gallery>=0.11.0,<0.15.0
+  - furo>=2022.9.29,<2023.10.0
+  - numpydoc>=1.5.0,<1.6
+  - sphinx-copybutton>=0.5.1,<0.5.3
+  - towncrier>=22.12.0,<23.7
+  - sphinxcontrib-mermaid>=0.8.1,<0.10
   - tox
   - ipykernel
   - pytest-cov
@@ -29,5 +29,5 @@ dependencies:
   - codespell
   - pip
   - pip:
-    - datalad>=0.15.4,<0.19
-    - julearn==0.2.5
+    - datalad>=0.15.4,<0.20
+    - julearn==0.3.0

docs/changes/newsfragments/253.misc

@@ -0,0 +1 @@
+Update dependencies requirements by `Fede Raimondo`_

docs/contribution.rst

@@ -171,7 +171,7 @@ Writing Examples
 The format used for text is reST. Check the `sphinx reST reference`_ for more
 details. The examples are run and displayed in HTML format using
 `sphinx gallery`_. To add an example, just create a ``.py`` file that starts
-either with ``plot_`` or ``run_``, dependending on whether the example generates
+either with ``plot_`` or ``run_``, depending on whether the example generates
 a figure or not.
 
 The first lines of the example should be a Python block comment with a title,

docs/installation.rst

@@ -10,14 +10,14 @@ Requirements
 junifer is compatible with `Python`_ >= 3.8 and requires the following packages:
 
 * ``click>=8.1.3,<8.2``
-* ``numpy>=1.22,<1.24``
-* ``datalad>=0.15.4,<0.19``
-* ``pandas>=1.4.0,<1.6``
-* ``nibabel>=3.2.0,<4.1``
-* ``nilearn>=0.9.0,<=0.10.0``
-* ``sqlalchemy>=1.4.27,<= 1.5.0``
+* ``numpy>=1.24,<1.27``
+* ``datalad>=0.15.4,<0.20``
+* ``pandas>=1.4.0,<2.2``
+* ``nibabel>=3.2.0,<5.11``
+* ``nilearn>=0.9.0,<=0.11.0``
+* ``sqlalchemy>=1.4.27,<= 2.1.0``
 * ``ruamel.yaml>=0.17,<0.18``
-* ``h5py>=3.8.0,<3.9``
+* ``h5py>=3.8.0,<3.10``
 
 Depending on the installation method, these packages might be installed
 automatically.

ignore_words.txt

@@ -2,3 +2,4 @@ master
 nin
 chang
 sepulcre
+arange

junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -397,6 +397,10 @@ class JuniferNiftiSpheresMasker(NiftiSpheresMasker):
 
         params = get_params(NiftiSpheresMasker, self)
 
+        # New in nilearn 0.10.1
+        if hasattr(self, "clean_kwargs"):
+            params["clean_kwargs"] = self.clean_kwargs
+
         signals, _ = self._cache(
             _filter_and_extract, ignore=["verbose", "memory", "memory_level"]
         )(

pyproject.toml

@@ -40,15 +40,15 @@ classifiers = [
 ]
 dependencies = [
     "click>=8.1.3,<8.2",
-    "numpy>=1.24,<1.26",
-    "datalad>=0.15.4,<0.19",
-    "pandas>=1.4.0,<1.6",
-    "nibabel>=3.2.0,<4.1",
-    "nilearn>=0.9.0,<=0.10.0",
-    "sqlalchemy>=1.4.27,<= 1.5.0",
+    "numpy>=1.24,<1.27",
+    "datalad>=0.15.4,<0.20",
+    "pandas>=1.4.0,<2.2",
+    "nibabel>=3.2.0,<5.11",
+    "nilearn>=0.9.0,<=0.11.0",
+    "sqlalchemy>=1.4.27,<= 2.1.0",
     "ruamel.yaml>=0.17,<0.18",
     "importlib_metadata; python_version < '3.10'",
-    "h5py>=3.8.0,<3.9",
+    "h5py>=3.8.0,<3.10",
 ]
 dynamic = ["version"]
 
@@ -63,15 +63,15 @@ junifer = "junifer.api.cli:cli"
 [project.optional-dependencies]
 dev = ["tox", "pre-commit"]
 docs = [
-    "seaborn>=0.11.2,<0.12",
-    "Sphinx>=5.3.0,<5.4",
-    "sphinx-gallery>=0.11.0,<0.12",
-    "furo>=2022.9.29,<2023.0.0",
+    "seaborn>=0.11.2,<0.13",
+    "sphinx>=5.3.0,<7.3",
+    "sphinx-gallery>=0.11.0,<0.15.0",
+    "furo>=2022.9.29,<2023.10.0",
     "numpydoc>=1.5.0,<1.6",
-    "julearn==0.3.0",
-    "sphinx-copybutton==0.5.1",
-    "towncrier==22.12.0",
-    "sphinxcontrib-mermaid==0.8.1",
+    "julearn>=0.3.0,<0.4",
+    "sphinx-copybutton>=0.5.1,<0.5.3",
+    "towncrier>=22.12.0,<23.7",
+    "sphinxcontrib-mermaid>=0.8.1,<0.10",
 ]
 onthefly = ["bctpy==0.6.0"]