MNT: Drop Python 3.8, update dependencies (#896)

* MNT: Drop Python 3.8 support

* Drop traits constraint

* Bump dependencies

Author: effigies

.github/workflows/pythonpackage.yml

@@ -122,14 +122,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         install: [repo]
         include:
-          - python-version: "3.11"
+          - python-version: "3.12"
             install: sdist
-          - python-version: "3.11"
+          - python-version: "3.12"
             install: wheel
-          - python-version: "3.11"
+          - python-version: "3.12"
             install: editable
 
     env:
@@ -201,7 +201,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        # Only run --pre tests on Python versions within SPEC0 support
+        python-version: ["3.11", "3.12"]
         install: [repo]
         pip-flags: ['--pre']
 

env.yml

@@ -10,13 +10,13 @@ dependencies:
   - mkl-service=2.4
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
-  - scipy=1.11
-  - matplotlib=3.8
+  - scipy=1.14
+  - matplotlib=3.9
   - pandas=2.2
-  - h5py=3.10
+  - h5py=3.12
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.22
-  - scikit-learn=1.4
+  - scikit-image=0.24
+  - scikit-learn=1.5
   # Utilities
   - graphviz=9.0
   # Workflow dependencies: ANTs

pyproject.toml

@@ -8,15 +8,14 @@ dynamic = ["version"]
 description = "NeuroImaging Workflows provides processing tools for magnetic resonance images of the brain."
 readme = "README.rst"
 license = {file = "LICENSE"}
-requires-python = ">= 3.8"
+requires-python = ">= 3.9"
 authors = [
     { name = "The NiPreps Developers", email = "[email protected]" },
 ]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -44,7 +43,6 @@ dependencies = [
     "seaborn",
     "svgutils >= 0.3.4",
     "templateflow >= 0.7.2",
-    "traits < 6.4",
     "transforms3d",
 ]
 

requirements.txt

@@ -1,84 +1,111 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile pyproject.toml -c - -p 3.11 -o requirements.txt
+#    uv pip compile pyproject.toml -p 3.11 -o requirements.txt
+acres==0.1.0
+    # via niworkflows (pyproject.toml)
 astor==0.8.1
     # via formulaic
-attrs==23.2.0
-bids-validator==1.14.1
+attrs==24.2.0
+    # via
+    #   niworkflows (pyproject.toml)
+    #   jsonschema
+    #   referencing
+bids-validator==1.14.7.post0
     # via pybids
-certifi==2024.7.4
+bidsschematools==0.11.3
+    # via bids-validator
+certifi==2024.8.30
     # via requests
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 ci-info==0.3.0
     # via etelemetry
 click==8.1.7
     # via
+    #   bidsschematools
     #   nipype
     #   pybids
-contourpy==1.2.0
+contourpy==1.3.0
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
 docopt==0.6.2
     # via num2words
 etelemetry==0.3.1
     # via nipype
-filelock==3.13.1
+filelock==3.16.1
     # via nipype
-fonttools==4.49.0
+fonttools==4.54.1
     # via matplotlib
 formulaic==0.5.2
     # via pybids
-greenlet==3.0.3
+fsspec==2024.10.0
+    # via universal-pathlib
+greenlet==3.1.1
     # via sqlalchemy
-h5py==3.10.0
+h5py==3.12.1
     # via nitransforms
-idna==3.6
+idna==3.10
     # via requests
-imageio==2.34.0
+imageio==2.36.0
     # via scikit-image
+importlib-resources==6.4.5
+    # via nibabel
 interface-meta==1.3.0
     # via formulaic
 isodate==0.6.1
     # via rdflib
-jinja2==3.1.3
-joblib==1.3.2
+jinja2==3.1.4
+    # via niworkflows (pyproject.toml)
+joblib==1.4.2
     # via
     #   nilearn
     #   scikit-learn
-kiwisolver==1.4.5
+jsonschema==4.23.0
+    # via bidsschematools
+jsonschema-specifications==2024.10.1
+    # via jsonschema
+kiwisolver==1.4.7
     # via matplotlib
-lazy-loader==0.3
+lazy-loader==0.4
     # via scikit-image
 looseversion==1.3.0
-    # via nipype
-lxml==5.1.0
+    # via
+    #   niworkflows (pyproject.toml)
+    #   nipype
+lxml==5.3.0
     # via
     #   nilearn
     #   prov
     #   svgutils
-markupsafe==2.1.5
+markupsafe==3.0.2
     # via jinja2
-matplotlib==3.8.3
-    # via seaborn
-networkx==3.2.1
+matplotlib==3.9.2
+    # via
+    #   niworkflows (pyproject.toml)
+    #   seaborn
+networkx==3.4.2
     # via
     #   nipype
     #   prov
     #   scikit-image
-nibabel==5.2.1
+nibabel==5.3.2
     # via
+    #   niworkflows (pyproject.toml)
     #   nilearn
     #   nipype
     #   nitransforms
     #   pybids
-nilearn==0.10.3
-nipype==1.8.6
-nitransforms==23.0.1
+nilearn==0.10.4
+    # via niworkflows (pyproject.toml)
+nipype==1.9.0
+    # via niworkflows (pyproject.toml)
+nitransforms==24.0.2
+    # via niworkflows (pyproject.toml)
 num2words==0.5.13
     # via pybids
 numpy==1.26.4
     # via
+    #   niworkflows (pyproject.toml)
     #   contourpy
     #   formulaic
     #   h5py
@@ -95,32 +122,40 @@ numpy==1.26.4
     #   scipy
     #   seaborn
     #   tifffile
-packaging==23.2
+    #   transforms3d
+packaging==24.1
     # via
+    #   niworkflows (pyproject.toml)
     #   etelemetry
+    #   lazy-loader
     #   matplotlib
     #   nibabel
     #   nilearn
     #   nipype
     #   scikit-image
-pandas==2.2.1
+pandas==2.2.3
     # via
+    #   niworkflows (pyproject.toml)
     #   formulaic
     #   nilearn
     #   pybids
     #   seaborn
-pillow==10.2.0
+pillow==11.0.0
     # via
     #   imageio
     #   matplotlib
     #   scikit-image
-prov==2.0.0
+prov==2.0.1
     # via nipype
-pybids==0.16.4
-    # via templateflow
-pydot==2.0.0
+puremagic==1.28
     # via nipype
-pyparsing==3.1.2
+pybids==0.17.2
+    # via
+    #   niworkflows (pyproject.toml)
+    #   templateflow
+pydot==3.0.2
+    # via nipype
+pyparsing==3.2.0
     # via
     #   matplotlib
     #   pydot
@@ -131,23 +166,36 @@ python-dateutil==2.9.0.post0
     #   nipype
     #   pandas
     #   prov
-pytz==2024.1
+pytz==2024.2
     # via pandas
-pyyaml==6.0.1
-rdflib==7.0.0
+pyyaml==6.0.2
+    # via
+    #   niworkflows (pyproject.toml)
+    #   bidsschematools
+rdflib==6.3.2
     # via
     #   nipype
     #   prov
-requests==2.31.0
+referencing==0.35.1
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+requests==2.32.3
     # via
     #   etelemetry
     #   nilearn
     #   templateflow
-scikit-image==0.22.0
-scikit-learn==1.4.1.post1
+rpds-py==0.20.1
+    # via
+    #   jsonschema
+    #   referencing
+scikit-image==0.24.0
+    # via niworkflows (pyproject.toml)
+scikit-learn==1.5.2
     # via nilearn
-scipy==1.11.4
+scipy==1.14.1
     # via
+    #   niworkflows (pyproject.toml)
     #   formulaic
     #   nilearn
     #   nipype
@@ -156,32 +204,39 @@ scipy==1.11.4
     #   scikit-image
     #   scikit-learn
 seaborn==0.13.2
-simplejson==3.19.2
+    # via niworkflows (pyproject.toml)
+simplejson==3.19.3
     # via nipype
 six==1.16.0
     # via
     #   isodate
     #   python-dateutil
-sqlalchemy==2.0.28
+sqlalchemy==2.0.36
     # via pybids
 svgutils==0.3.4
-templateflow==24.0.0
-threadpoolctl==3.3.0
+    # via niworkflows (pyproject.toml)
+templateflow==24.2.2
+    # via niworkflows (pyproject.toml)
+threadpoolctl==3.5.0
     # via scikit-learn
-tifffile==2024.2.12
+tifffile==2024.9.20
     # via scikit-image
-tqdm==4.66.2
+tqdm==4.66.6
     # via templateflow
-traits==6.3.2
+traits==6.4.3
     # via nipype
-transforms3d==0.4.1
-typing-extensions==4.10.0
+transforms3d==0.4.2
+    # via niworkflows (pyproject.toml)
+typing-extensions==4.12.2
     # via
     #   formulaic
+    #   nibabel
     #   sqlalchemy
-tzdata==2024.1
+tzdata==2024.2
     # via pandas
-urllib3==2.2.1
+universal-pathlib==0.2.5
+    # via pybids
+urllib3==2.2.3
     # via requests
 wrapt==1.16.0
     # via formulaic