Merge pull request #3685 from effigies/mnt/traits

MNT: Drop traits upper bound

.circleci/config.yml

@@ -266,43 +266,4 @@ jobs:
 workflows:
   version: 2
   build_test_deploy:
-    jobs:
-      - compare_base_dockerfiles:
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-            tags:
-              only: /.*/
-      - get_test_data:
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-            tags:
-              only: /.*/
-      - test_pytest:
-          filters:
-            branches:
-              ignore:
-                - /docs?\/.*/
-            tags:
-              only: /.*/
-          requires:
-            - compare_base_dockerfiles
-            - get_test_data
-      - deploy_dockerhub:
-          filters:
-            branches:
-              only: master
-            tags:
-              only: /.*/
-          requires:
-            - test_pytest
-      - update_feedstock:
-          context: nipybot
-          filters:
-            branches:
-              only: /rel\/\d.*/
-            tags:
-              only: /.*/
+    jobs: []

.github/workflows/contrib.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: [3.8]
+        python-version: ["3.12"]
         nipype-extras: ["dev"]
         check: ["specs", "style"]
     env:

.github/workflows/tests.yml

@@ -91,22 +91,22 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-22.04"]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         check: ["test"]
         pip-flags: [""]
         depends: ["REQUIREMENTS"]
         deb-depends: [false]
         nipype-extras: ["doc,tests,profiler"]
         include:
           - os: ubuntu-22.04
-            python-version: "3.8"
+            python-version: "3.9"
             check: test
             pip-flags: ""
             depends: REQUIREMENTS
             deb-depends: true
             nipype-extras: doc,tests,profiler,duecredit,ssh
           - os: ubuntu-20.04
-            python-version: 3.8
+            python-version: "3.9"
             check: test
             pip-flags: ""
             depends: REQUIREMENTS

nipype/algorithms/confounds.py

@@ -24,6 +24,7 @@
     InputMultiPath,
     OutputMultiPath,
     SimpleInterface,
+    Tuple,
 )
 from ..utils.misc import normalize_mc_params
 
@@ -64,7 +65,7 @@ class ComputeDVARSInputSpec(BaseInterfaceInputSpec):
     series_tr = traits.Float(desc="repetition time in sec.")
     save_plot = traits.Bool(False, usedefault=True, desc="write DVARS plot")
     figdpi = traits.Int(100, usedefault=True, desc="output dpi for the plot")
-    figsize = traits.Tuple(
+    figsize = Tuple(
         traits.Float(11.7),
         traits.Float(2.3),
         usedefault=True,
@@ -286,7 +287,7 @@ class FramewiseDisplacementInputSpec(BaseInterfaceInputSpec):
     save_plot = traits.Bool(False, usedefault=True, desc="write FD plot")
     normalize = traits.Bool(False, usedefault=True, desc="calculate FD in mm/s")
     figdpi = traits.Int(100, usedefault=True, desc="output dpi for the FD plot")
-    figsize = traits.Tuple(
+    figsize = Tuple(
         traits.Float(11.7),
         traits.Float(2.3),
         usedefault=True,

nipype/algorithms/mesh.py

@@ -14,6 +14,7 @@
     TraitedSpec,
     File,
     BaseInterfaceInputSpec,
+    Tuple,
 )
 from ..interfaces.vtkbase import tvtk
 from ..interfaces import vtkbase as VTKInfo
@@ -289,7 +290,7 @@ class MeshWarpMathsInputSpec(BaseInterfaceInputSpec):
     )
     float_trait = traits.Either(
         traits.Float(1.0),
-        traits.Tuple(traits.Float(1.0), traits.Float(1.0), traits.Float(1.0)),
+        Tuple(traits.Float(1.0), traits.Float(1.0), traits.Float(1.0)),
     )
 
     operator = traits.Either(

nipype/algorithms/misc.py

@@ -23,6 +23,7 @@
     isdefined,
     DynamicTraitedSpec,
     Undefined,
+    Tuple,
 )
 from ..utils.filemanip import fname_presuffix, split_filename, ensure_list
 
@@ -1176,7 +1177,7 @@ def _list_outputs(self):
 class SplitROIsInputSpec(TraitedSpec):
     in_file = File(exists=True, mandatory=True, desc="file to be split")
     in_mask = File(exists=True, desc="only process files inside mask")
-    roi_size = traits.Tuple(traits.Int, traits.Int, traits.Int, desc="desired ROI size")
+    roi_size = Tuple(traits.Int, traits.Int, traits.Int, desc="desired ROI size")
 
 
 class SplitROIsOutputSpec(TraitedSpec):

nipype/info.py

@@ -54,14 +54,13 @@ def get_nipype_gitversion():
     "License :: OSI Approved :: Apache Software License",
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering",
 ]
-PYTHON_REQUIRES = ">= 3.8"
+PYTHON_REQUIRES = ">= 3.9"
 
 description = "Neuroimaging in Python: Pipelines and Interfaces"
 
@@ -103,9 +102,9 @@ def get_nipype_gitversion():
 NIBABEL_MIN_VERSION = "2.1.0"
 NETWORKX_MIN_VERSION = "2.0"
 NUMPY_MIN_VERSION = "1.17"
+NUMPY_MAX_VERSION = "2.0"
 SCIPY_MIN_VERSION = "0.14"
 TRAITS_MIN_VERSION = "4.6"
-TRAITS_MAX_VERSION = "6.4"
 DATEUTIL_MIN_VERSION = "2.2"
 SIMPLEJSON_MIN_VERSION = "3.8.0"
 PROV_MIN_VERSION = "1.5.2"
@@ -137,15 +136,15 @@ def get_nipype_gitversion():
     "click>=%s" % CLICK_MIN_VERSION,
     "networkx>=%s" % NETWORKX_MIN_VERSION,
     "nibabel>=%s" % NIBABEL_MIN_VERSION,
-    "numpy>=%s" % NUMPY_MIN_VERSION,
+    "numpy>=%s,<%s" % (NUMPY_MIN_VERSION, NUMPY_MAX_VERSION),
     "packaging",
     "prov>=%s" % PROV_MIN_VERSION,
     "pydot>=%s" % PYDOT_MIN_VERSION,
     "python-dateutil>=%s" % DATEUTIL_MIN_VERSION,
     "rdflib>=%s" % RDFLIB_MIN_VERSION,
     "scipy>=%s" % SCIPY_MIN_VERSION,
     "simplejson>=%s" % SIMPLEJSON_MIN_VERSION,
-    "traits>=%s,<%s,!=5.0" % (TRAITS_MIN_VERSION, TRAITS_MAX_VERSION),
+    "traits>=%s,!=5.0" % TRAITS_MIN_VERSION,
     "filelock>=3.0.0",
     "etelemetry>=0.2.0",
     "looseversion!=1.2",

nipype/interfaces/afni/model.py

@@ -22,6 +22,7 @@
     InputMultiPath,
     Undefined,
     Str,
+    Tuple,
 )
 from ...external.due import BibTeX
 
@@ -127,7 +128,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         "that 'gotforit' is needed to ignore.",
         argstr="-allzero_OK",
     )
-    dname = traits.Tuple(
+    dname = Tuple(
         Str, Str, desc="set environmental variable to provided value", argstr="-D%s=%s"
     )
     mask = File(
@@ -162,7 +163,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         "[default: 1]",
         argstr="-polort %d",
     )
-    ortvec = traits.Tuple(
+    ortvec = Tuple(
         File(desc="filename", exists=True),
         Str(desc="label"),
         desc="this option lets you input a rectangular array of 1 or more "
@@ -213,7 +214,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         desc="number of stimulus timing files", argstr="-num_stimts %d", position=-6
     )
     stim_times = traits.List(
-        traits.Tuple(
+        Tuple(
             traits.Int(desc="k-th response model"),
             File(desc="stimulus timing file", exists=True),
             Str(desc="model"),
@@ -223,9 +224,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         position=-5,
     )
     stim_label = traits.List(
-        traits.Tuple(
-            traits.Int(desc="k-th input stimulus"), Str(desc="stimulus label")
-        ),
+        Tuple(traits.Int(desc="k-th input stimulus"), Str(desc="stimulus label")),
         desc="label for kth input stimulus (e.g., Label1)",
         argstr="-stim_label %d %s...",
         requires=["stim_times"],
@@ -251,9 +250,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         position=-2,
     )
     glt_label = traits.List(
-        traits.Tuple(
-            traits.Int(desc="k-th general linear test"), Str(desc="GLT label")
-        ),
+        Tuple(traits.Int(desc="k-th general linear test"), Str(desc="GLT label")),
         desc="general linear test (i.e., contrast) labels",
         argstr="-glt_label %d %s...",
         requires=["gltsym"],
@@ -488,9 +485,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         argstr="-nobout",
     )
     gltsym = traits.List(
-        traits.Either(
-            traits.Tuple(File(exists=True), Str()), traits.Tuple(Str(), Str())
-        ),
+        traits.Either(Tuple(File(exists=True), Str()), Tuple(Str(), Str())),
         desc="read a symbolic GLT from input file and associate it with a "
         "label. As in Deconvolve, you can also use the 'SYM:' method "
         "to provide the definition of the GLT directly as a string "

nipype/interfaces/afni/preprocess.py

@@ -11,6 +11,7 @@
     CommandLine,
     TraitedSpec,
     traits,
+    Tuple,
     isdefined,
     File,
     InputMultiPath,
@@ -2439,7 +2440,7 @@ class TCorrMapInputSpec(AFNICommandInputSpec):
     mask = File(exists=True, argstr="-mask %s")
     automask = traits.Bool(argstr="-automask")
     polort = traits.Int(argstr="-polort %d")
-    bandpass = traits.Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
+    bandpass = Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
     regress_out_timeseries = File(exists=True, argstr="-ort %s")
     blur_fwhm = traits.Float(argstr="-Gblur %f")
     seeds_width = traits.Float(argstr="-Mseed %f", xor=("seeds"))
@@ -3011,13 +3012,13 @@ class TProjectInputSpec(AFNICommandInputSpec):
 
 """,
     )
-    bandpass = traits.Tuple(
+    bandpass = Tuple(
         traits.Float,
         traits.Float,
         desc="""Remove all frequencies EXCEPT those in the range""",
         argstr="-bandpass %g %g",
     )
-    stopband = traits.Tuple(
+    stopband = Tuple(
         traits.Float,
         traits.Float,
         desc="""Remove all frequencies in the range""",
@@ -3394,7 +3395,7 @@ class VolregInputSpec(AFNICommandInputSpec):
         copyfile=False,
     )
     in_weight_volume = traits.Either(
-        traits.Tuple(File(exists=True), traits.Int),
+        Tuple(File(exists=True), traits.Int),
         File(exists=True),
         desc="weights for each voxel specified by a file with an "
         "optional volume number (defaults to 0)",
@@ -3821,8 +3822,8 @@ class QwarpInputSpec(AFNICommandInputSpec):
         maxlen=5,
         xor=["wmask"],
     )
-    traits.Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
-    wmask = traits.Tuple(
+    bandpass = Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
+    wmask = Tuple(
         (File(exists=True), traits.Float()),
         desc="""\
 Similar to '-wball', but here, you provide a dataset 'ws'

nipype/interfaces/afni/tests/test_auto_Qwarp.py

@@ -28,6 +28,9 @@ def test_Qwarp_inputs():
             argstr="-ballopt",
             xor=["workhard", "boxopt"],
         ),
+        bandpass=dict(
+            argstr="-bpass %f %f",
+        ),
         base_file=dict(
             argstr="-base %s",
             copyfile=False,

nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py

@@ -28,6 +28,9 @@ def test_QwarpPlusMinus_inputs():
             argstr="-ballopt",
             xor=["workhard", "boxopt"],
         ),
+        bandpass=dict(
+            argstr="-bpass %f %f",
+        ),
         base_file=dict(
             argstr="-base %s",
             copyfile=False,