diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
deleted file mode 100644
index 6b3ef96f0c..0000000000
--- a/.github/workflows/contrib.yml
+++ /dev/null
@@ -1,84 +0,0 @@
-name: Contribution checks
-
-# This checks validate contributions meet baseline checks
-#
-# * specs - Ensure make
-
-on:
-  push:
-    branches:
-      - master
-      - maint/*
-  pull_request:
-    branches:
-      - master
-      - maint/*
-
-defaults:
-  run:
-    shell: bash
-
-concurrency:
-  group: contrib-${{ github.ref }}
-  cancel-in-progress: true
-
-permissions:
-  contents: read # to fetch code (actions/checkout)
-
-jobs:
-  stable:
-    # Check each OS, all supported Python, minimum versions and latest releases
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: ["ubuntu-latest"]
-        python-version: ["3.12"]
-        nipype-extras: ["dev"]
-        check: ["specs", "style"]
-    env:
-      DEPENDS: ""
-      CHECK_TYPE: ${{ matrix.check }}
-      NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
-      EXTRA_PIP_FLAGS: ""
-      INSTALL_DEB_DEPENDENCIES: false
-      INSTALL_TYPE: pip
-      CI_SKIP_TEST: 1
-
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: recursive
-          fetch-depth: 0
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
-      - name: Create virtual environment
-        run: tools/ci/create_venv.sh
-      - name: Build archive
-        run: |
-          source tools/ci/build_archive.sh
-          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
-      - name: Install Debian dependencies
-        run: tools/ci/install_deb_dependencies.sh
-        if: ${{ matrix.os == 'ubuntu-18.04' }}
-      - name: Install dependencies
-        run: tools/ci/install_dependencies.sh
-      - name: Install Nipype
-        run: tools/ci/install.sh
-      - name: Run tests
-        run: tools/ci/check.sh
-        if: ${{ matrix.check != 'skiptests' }}
-      - uses: codecov/codecov-action@v4
-        with:
-          file: coverage.xml
-          token: ${{ secrets.CODECOV_TOKEN }}
-        if: ${{ always() }}
-      - name: Upload pytest test results
-        uses: actions/upload-artifact@v4
-        with:
-          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
-          path: test-results.xml
-        if: ${{ always() && matrix.check == 'test' }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 41776bc188..ee5786af8f 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,22 +1,11 @@
-name: Stable tests
-
-# This file tests the claimed support range of nipype including
-#
-# * Operating systems: Linux, OSX
-# * Dependencies: minimum requirements, optional requirements
-# * Installation methods: setup.py, sdist, wheel, archive
+name: Tox
 
 on:
   push:
-    branches:
-      - master
-      - maint/*
-    tags:
-      - "*"
+    branches: [ master, main, 'maint/*' ]
+    tags: [ '*' ]
   pull_request:
-    branches:
-      - master
-      - maint/*
+    branches: [ master, main, 'maint/*' ]
   schedule:
     # 8am EST / 9am EDT Mondays
     - cron: "0 13 * * 1"
@@ -26,27 +15,28 @@ defaults:
     shell: bash
 
 concurrency:
-  group: tests-${{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-permissions: {}
+permissions:
+  contents: read
+
+env:
+  # Force tox and pytest to use color
+  FORCE_COLOR: true
+
+
 jobs:
   build:
-    permissions:
-      contents: read # to fetch code (actions/checkout)
-
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3
-      - run: pip install --upgrade build twine
-      - name: Build sdist and wheel
-        run: python -m build
-      - run: twine check dist/*
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v3
+      - run: uv build
+      - run: uvx twine check dist/*
       - uses: actions/upload-artifact@v4
         with:
           name: dist
@@ -82,72 +72,52 @@ jobs:
       - name: Run tests
         run: pytest --doctest-modules -v --pyargs nipype
 
-  stable:
+  test:
     # Check each OS, all supported Python, minimum versions and latest releases
-    permissions:
-      contents: read # to fetch code (actions/checkout)
-
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["ubuntu-22.04"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        check: ["test"]
-        pip-flags: [""]
-        depends: ["REQUIREMENTS"]
-        deb-depends: [false]
-        nipype-extras: ["doc,tests,profiler"]
+        os: ["ubuntu-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        dependencies: [none, full, pre]
         include:
-          - os: ubuntu-22.04
+          - os: ubuntu-latest
             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: "3.9"
-            check: test
-            pip-flags: ""
-            depends: REQUIREMENTS
-            deb-depends: true
-            nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
+            dependencies: min
+        exclude:
+          # Skip some intermediate versions for full tests
+          - python-version: "3.10"
+            dependencies: full
+          - python-version: "3.11"
+            dependencies: full
+          # Do not test pre-releases for versions out of SPEC0
+          - python-version: "3.9"
+            dependencies: pre
+          - python-version: "3.10"
+            dependencies: pre
+
     env:
-      DEPENDS: ${{ matrix.depends }}
-      CHECK_TYPE: ${{ matrix.check }}
-      EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
-      INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
-      NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
-      INSTALL_TYPE: pip
-      CI_SKIP_TEST: 1
+      DEPENDS: ${{ matrix.dependencies }}
 
     steps:
       - uses: actions/checkout@v4
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-      - name: Create virtual environment
-        run: tools/ci/create_venv.sh
-      - name: Build archive
+      - name: Install tox
         run: |
-          source tools/ci/build_archive.sh
-          echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
-      - name: Install Debian dependencies
-        run: tools/ci/install_deb_dependencies.sh
-        if: ${{ matrix.os == 'ubuntu-latest' }}
-      - name: Install dependencies
-        run: tools/ci/install_dependencies.sh
-      - name: Install Nipype
-        run: tools/ci/install.sh
-      - name: Run tests
-        run: tools/ci/check.sh
-        if: ${{ matrix.check != 'skiptests' }}
+          uv tool install tox --with=tox-uv --with=tox-gh-actions
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v --exit-and-dump-after 1200
       - uses: codecov/codecov-action@v4
         with:
-          file: coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
       - name: Upload pytest test results
@@ -160,7 +130,7 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     environment: "Package deployment"
-    needs: [stable, test-package]
+    needs: [test, test-package]
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
       - uses: actions/download-artifact@v4
@@ -171,3 +141,21 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}
+
+  checks:
+    runs-on: 'ubuntu-latest'
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ['specs', 'style']
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v3
+      - name: Show tox config
+        run: uvx tox c
+      - name: Show tox config (this call)
+        run: uvx tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: uvx tox -e ${{ matrix.check }}
diff --git a/.mailmap b/.mailmap
index 4c5bd5de4d..35ccbf89d2 100644
--- a/.mailmap
+++ b/.mailmap
@@ -107,6 +107,7 @@ Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> <jstadler@ilin-magdeburg.de>
 Joerg Stadler <Joerg.Stadler@lin-magdeburg.de> <Stadler@lin-magdeburg.de>
 John A. Lee <johnleenimh@gmail.com>
 John A. Lee <johnleenimh@gmail.com> <leej3@users.noreply.github.com>
+Jon Cluce <jon.clucas@childmind.org>
 Joke Durnez <joke.durnez@gmail.com>
 Jordi Huguet <jhuguetn@gmail.com>
 Josh Warner <silvertrumpet999+github@gmail.com> <warner.joshua@mayo.edu>
diff --git a/.zenodo.json b/.zenodo.json
index 5ddb9a71dd..3e2c2be6f6 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -285,6 +285,11 @@
     {
       "name": "Mordom, David"
     },
+    {
+      "affiliation": "Child Mind Institute",
+      "name": "Cluce, Jon",
+      "orcid": "0000-0001-7590-5806"
+    },
     {
       "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
       "name": "Guillon, Jérémy",
diff --git a/doc/changelog/1.X.X-changelog.rst b/doc/changelog/1.X.X-changelog.rst
index b150eece35..79b583c871 100644
--- a/doc/changelog/1.X.X-changelog.rst
+++ b/doc/changelog/1.X.X-changelog.rst
@@ -1,8 +1,21 @@
+1.9.1 (November 19, 2024)
+=========================
+
+Bug fix release in the 1.9.x series.
+
+This release adds support for Numpy 2 and Python 3.13.
+
+  * FIX: Restore generate_gantt_chart functionality (https://github.com/nipy/nipype/pull/3290)
+  * FIX: Address numpy and traits deprecations (https://github.com/nipy/nipype/pull/3699)
+  * FIX: `ts_Z_corr` → `ts_wb_Z` (https://github.com/nipy/nipype/pull/3697)
+  * ENH: Remove unused and recently unsupported antsRegistration flag (https://github.com/nipy/nipype/pull/3695)
+  * MAINT: Bump codecov/codecov-action from 4 to 5 (https://github.com/nipy/nipype/pull/3698)
+
 
 1.9.0 (October 31, 2024)
 ========================
 
-New feature release in the 1.9.0 series.
+New feature release in the 1.9.x series.
 
   * FIX: Remove exists=True from fsl.MotionOutliers output that might not exist (https://github.com/nipy/nipype/pull/1428)
   * FIX: Improve evaluate_connect_function errors across Python versions (https://github.com/nipy/nipype/pull/3655)
diff --git a/doc/interfaces.rst b/doc/interfaces.rst
index e7b9dca2f4..4a8714e630 100644
--- a/doc/interfaces.rst
+++ b/doc/interfaces.rst
@@ -8,7 +8,7 @@ Interfaces and Workflows
 :Release: |version|
 :Date: |today|
 
-Previous versions: `1.8.6 <http://nipype.readthedocs.io/en/1.8.6/>`_ `1.8.5 <http://nipype.readthedocs.io/en/1.8.5/>`_
+Previous versions: `1.9.0 <http://nipype.readthedocs.io/en/1.9.0/>`_ `1.8.6 <http://nipype.readthedocs.io/en/1.8.6/>`_
 
 Workflows
 ---------
diff --git a/nipype/algorithms/confounds.py b/nipype/algorithms/confounds.py
index 157d1e48d7..5e3588f4fc 100644
--- a/nipype/algorithms/confounds.py
+++ b/nipype/algorithms/confounds.py
@@ -188,7 +188,7 @@ def _run_interface(self, runtime):
 
         if self.inputs.save_std:
             out_file = self._gen_fname("dvars_std", ext="tsv")
-            np.savetxt(out_file, dvars[0], fmt=b"%0.6f")
+            np.savetxt(out_file, dvars[0], fmt="%0.6f")
             self._results["out_std"] = out_file
 
             if self.inputs.save_plot:
@@ -228,7 +228,7 @@ def _run_interface(self, runtime):
 
         if self.inputs.save_vxstd:
             out_file = self._gen_fname("dvars_vxstd", ext="tsv")
-            np.savetxt(out_file, dvars[2], fmt=b"%0.6f")
+            np.savetxt(out_file, dvars[2], fmt="%0.6f")
             self._results["out_vxstd"] = out_file
 
             if self.inputs.save_plot:
@@ -251,8 +251,8 @@ def _run_interface(self, runtime):
             np.savetxt(
                 out_file,
                 np.vstack(dvars).T,
-                fmt=b"%0.8f",
-                delimiter=b"\t",
+                fmt="%0.8f",
+                delimiter="\t",
                 header="std DVARS\tnon-std DVARS\tvx-wise std DVARS",
                 comments="",
             )
@@ -689,7 +689,7 @@ def _run_interface(self, runtime):
         np.savetxt(
             components_file,
             components,
-            fmt=b"%.10f",
+            fmt="%.10f",
             delimiter="\t",
             header="\t".join(components_header),
             comments="",
@@ -729,7 +729,7 @@ def _run_interface(self, runtime):
             np.savetxt(
                 self._results["pre_filter_file"],
                 filter_basis,
-                fmt=b"%.10f",
+                fmt="%.10f",
                 delimiter="\t",
                 header="\t".join(header),
                 comments="",
diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py
index ff867ae26c..65aae2ef1c 100644
--- a/nipype/algorithms/rapidart.py
+++ b/nipype/algorithms/rapidart.py
@@ -189,7 +189,8 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
         desc="Source of movement parameters",
         mandatory=True,
     )
-    use_differences = traits.ListBool(
+    use_differences = traits.List(
+        traits.Bool,
         [True, False],
         minlen=2,
         maxlen=2,
@@ -600,10 +601,10 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
         outliers = np.unique(np.union1d(iidx, np.union1d(tidx, ridx)))
 
         # write output to outputfile
-        np.savetxt(artifactfile, outliers, fmt=b"%d", delimiter=" ")
-        np.savetxt(intensityfile, g, fmt=b"%.2f", delimiter=" ")
+        np.savetxt(artifactfile, outliers, fmt="%d", delimiter=" ")
+        np.savetxt(intensityfile, g, fmt="%.2f", delimiter=" ")
         if self.inputs.use_norm:
-            np.savetxt(normfile, normval, fmt=b"%.4f", delimiter=" ")
+            np.savetxt(normfile, normval, fmt="%.4f", delimiter=" ")
 
         if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
             import matplotlib
diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py
index 51010aea3a..4d5a7ca53b 100644
--- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py
+++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py
@@ -48,8 +48,6 @@ def test_ArtifactDetect_inputs():
             xor=["norm_threshold"],
         ),
         use_differences=dict(
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         use_norm=dict(
diff --git a/nipype/conftest.py b/nipype/conftest.py
index 18b8a1ca6d..151906678f 100644
--- a/nipype/conftest.py
+++ b/nipype/conftest.py
@@ -2,7 +2,7 @@
 import shutil
 from tempfile import mkdtemp
 import pytest
-import numpy
+import numpy as np
 import py.path as pp
 
 NIPYPE_DATADIR = os.path.realpath(
@@ -15,12 +15,17 @@
 
 @pytest.fixture(autouse=True)
 def add_np(doctest_namespace):
-    doctest_namespace["np"] = numpy
+    doctest_namespace["np"] = np
     doctest_namespace["os"] = os
     doctest_namespace["pytest"] = pytest
     doctest_namespace["datadir"] = data_dir
 
 
+@pytest.fixture(scope='session', autouse=True)
+def legacy_printoptions():
+    np.set_printoptions(legacy='1.21')
+
+
 @pytest.fixture(autouse=True)
 def _docdir(request):
     """Grabbed from https://stackoverflow.com/a/46991331"""
diff --git a/nipype/info.py b/nipype/info.py
index 3b006ae161..d5ddd6bfb8 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove .dev0 for release
-__version__ = "1.9.0"
+__version__ = "1.9.1"
 
 
 def get_nipype_gitversion():
@@ -99,12 +99,11 @@ def get_nipype_gitversion():
 """
 
 # versions
-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"
+NIBABEL_MIN_VERSION = "3.0"
+NETWORKX_MIN_VERSION = "2.5"
+NUMPY_MIN_VERSION = "1.21"
+SCIPY_MIN_VERSION = "1.8"
+TRAITS_MIN_VERSION = "6.2"
 DATEUTIL_MIN_VERSION = "2.2"
 SIMPLEJSON_MIN_VERSION = "3.8.0"
 PROV_MIN_VERSION = "1.5.2"
@@ -136,7 +135,7 @@ def get_nipype_gitversion():
     "click>=%s" % CLICK_MIN_VERSION,
     "networkx>=%s" % NETWORKX_MIN_VERSION,
     "nibabel>=%s" % NIBABEL_MIN_VERSION,
-    "numpy>=%s,<%s" % (NUMPY_MIN_VERSION, NUMPY_MAX_VERSION),
+    "numpy>=%s" % NUMPY_MIN_VERSION,
     "packaging",
     "prov>=%s" % PROV_MIN_VERSION,
     "pydot>=%s" % PYDOT_MIN_VERSION,
@@ -144,22 +143,24 @@ def get_nipype_gitversion():
     "rdflib>=%s" % RDFLIB_MIN_VERSION,
     "scipy>=%s" % SCIPY_MIN_VERSION,
     "simplejson>=%s" % SIMPLEJSON_MIN_VERSION,
-    "traits>=%s,!=5.0" % TRAITS_MIN_VERSION,
+    "traits>=%s" % TRAITS_MIN_VERSION,
     "filelock>=3.0.0",
-    "etelemetry>=0.2.0",
+    "acres",
+    "etelemetry>=0.3.1",
     "looseversion!=1.2",
     "puremagic",
 ]
 
 TESTS_REQUIRES = [
-    "codecov",
-    "coverage",
-    "pytest",
-    "pytest-cov",
+    "coverage >= 5.2.1",
+    "pandas >= 1.5.0",
+    "pytest >= 6",
+    "pytest-cov >=2.11",
     "pytest-env",
-    "pytest-timeout",
+    "pytest-timeout >=1.4",
     "pytest-doctestplus",
-    "sphinx",
+    "pytest-xdist >= 2.5",
+    "sphinx >=7",
 ]
 
 EXTRA_REQUIRES = {
diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
index d3daebcf4c..b5e27ea53a 100644
--- a/nipype/interfaces/afni/preprocess.py
+++ b/nipype/interfaces/afni/preprocess.py
@@ -2741,7 +2741,7 @@ def _list_outputs(self):
         odir = os.path.dirname(os.path.abspath(prefix))
         outputs["out_corr_matrix"] = glob.glob(os.path.join(odir, "*.netcc"))[0]
 
-        if isdefined(self.inputs.ts_wb_corr) or isdefined(self.inputs.ts_Z_corr):
+        if self.inputs.ts_wb_corr or self.inputs.ts_wb_Z:
             corrdir = os.path.join(odir, prefix + "_000_INDIV")
             outputs["out_corr_maps"] = glob.glob(os.path.join(corrdir, "*.nii.gz"))
 
diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py
index 41037ffc5f..91b131bbf3 100644
--- a/nipype/interfaces/ants/registration.py
+++ b/nipype/interfaces/ants/registration.py
@@ -710,9 +710,9 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
+--use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1'
     >>> reg.run()  # doctest: +SKIP
 
@@ -726,9 +726,9 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
+--use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.025, 1.0 ]  --write-composite-transform 1'
     >>> reg1.run()  # doctest: +SKIP
 
@@ -742,9 +742,9 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
+--use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 0.975 ]  --write-composite-transform 1'
 
     Clip extremely low intensity data points using winsorize_lower_quantile. All data points
@@ -759,9 +759,9 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
+--use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.025, 0.975 ]  --write-composite-transform 1'
 
     Use float instead of double for computations (saves memory usage)
@@ -773,10 +773,10 @@ class Registration(ANTSCommand):
 --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear \
 --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] \
---smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 \
+--smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-histogram-matching 1 \
 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] \
 --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
+--use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
 --write-composite-transform 1'
 
     Force to use double instead of float for computations (more precision and memory usage).
@@ -788,10 +788,10 @@ class Registration(ANTSCommand):
 --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear \
 --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] \
---smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 \
+--smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-histogram-matching 1 \
 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] \
 --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
+--use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
 --write-composite-transform 1'
 
     'collapse_output_transforms' can be used to put all transformation in a single 'composite_transform'-
@@ -823,10 +823,10 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 1 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --restore-state trans.mat --save-state trans.mat --transform Affine[ 2.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] \
---smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 \
+--smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-histogram-matching 1 \
 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] \
 --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
+--use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
 --write-composite-transform 1'
 
 
@@ -857,10 +857,10 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 1 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --restore-state trans.mat --save-state trans.mat --transform Affine[ 2.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] \
---smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 \
+--smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-histogram-matching 1 \
 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] \
 --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
+--use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
 --write-composite-transform 0'
 
     One can use multiple similarity metrics in a single registration stage.The Node below first
@@ -885,10 +885,10 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
+--use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 0.5, 32, None, 0.05 ] \
 --metric CC[ fixed1.nii, moving1.nii, 0.5, 4, None, 0.1 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1'
 
     ANTS Registration can also use multiple modalities to perform the registration. Here it is assumed
@@ -906,10 +906,10 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
+--use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 0.5, 32, None, 0.05 ] \
 --metric CC[ fixed2.nii, moving2.nii, 0.5, 4, None, 0.1 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1'
 
     Different methods can be used for the interpolation when applying transformations.
@@ -923,9 +923,9 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation BSpline[ 3 ] --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
+--use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1'
 
     >>> # Test Interpolation Parameters (MultiLabel/Gaussian)
@@ -937,10 +937,10 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Gaussian[ 1.0, 1.0 ] \
 --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] \
---smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 \
+--smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-histogram-matching 1 \
 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] \
 --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
+--use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
 --write-composite-transform 1'
 
     BSplineSyN non-linear registration with custom parameters.
@@ -954,9 +954,9 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform BSplineSyN[ 0.25, 26, 0, 3 ] \
+--use-histogram-matching 1 --transform BSplineSyN[ 0.25, 26, 0, 3 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] \
---smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 \
+--smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1'
 
     Mask the fixed image in the second stage of the registration (but not the first).
@@ -969,10 +969,10 @@ class Registration(ANTSCommand):
 --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \
 --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \
 --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --masks [ NULL, NULL ] \
+--use-histogram-matching 1 --masks [ NULL, NULL ] \
 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] \
 --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --masks [ fixed1.nii, NULL ] \
+--use-histogram-matching 1 --masks [ fixed1.nii, NULL ] \
 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1'
 
     Here we use both a warpfield and a linear transformation, before registration commences.  Note that
@@ -988,10 +988,10 @@ class Registration(ANTSCommand):
 [ func_to_struct.mat, 0 ] [ ants_Warp.nii.gz, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear \
 --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] \
 --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] \
---smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 \
+--smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-histogram-matching 1 \
 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] \
 --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 \
---use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
+--use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  \
 --write-composite-transform 1'
     """
 
@@ -1155,10 +1155,9 @@ def _format_registration(self):
                 % self._format_xarray(self.inputs.shrink_factors[ii])
             )
             if isdefined(self.inputs.use_estimate_learning_rate_once):
-                retval.append(
-                    "--use-estimate-learning-rate-once %d"
-                    % self.inputs.use_estimate_learning_rate_once[ii]
-                )
+                # this flag was removed because it was never used in the ants codebase
+                # removed from Ants in commit e1e47994b on 2022-08-09
+                pass
             if isdefined(self.inputs.use_histogram_matching):
                 # use_histogram_matching is either a common flag for all transforms
                 # or a list of transform-specific flags
diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py
index 3c87b71975..47592d70b5 100644
--- a/nipype/interfaces/ants/segmentation.py
+++ b/nipype/interfaces/ants/segmentation.py
@@ -1328,7 +1328,8 @@ class JointFusionInputSpec(ANTSCommandInputSpec):
         usedefault=True,
         desc=("Constrain solution to non-negative weights."),
     )
-    patch_radius = traits.ListInt(
+    patch_radius = traits.List(
+        traits.Int,
         minlen=3,
         maxlen=3,
         argstr="-p %s",
diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py
index f234ceea7c..98d8d696a1 100644
--- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py
+++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py
@@ -70,8 +70,6 @@ def test_JointFusion_inputs():
         ),
         patch_radius=dict(
             argstr="-p %s",
-            maxlen=3,
-            minlen=3,
         ),
         retain_atlas_voting_images=dict(
             argstr="-f",
diff --git a/nipype/interfaces/base/__init__.py b/nipype/interfaces/base/__init__.py
index 2e54847958..2af425d284 100644
--- a/nipype/interfaces/base/__init__.py
+++ b/nipype/interfaces/base/__init__.py
@@ -7,7 +7,8 @@
 This module defines the API of all nipype interfaces.
 
 """
-from traits.trait_handlers import TraitDictObject, TraitListObject
+from traits.trait_dict_object import TraitDictObject
+from traits.trait_list_object import TraitListObject
 from traits.trait_errors import TraitError
 
 from .core import (
diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index a7f61e6889..defbca7f43 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -15,7 +15,8 @@
 from packaging.version import Version
 
 from traits.trait_errors import TraitError
-from traits.trait_handlers import TraitDictObject, TraitListObject
+from traits.trait_dict_object import TraitDictObject
+from traits.trait_list_object import TraitListObject
 from ...utils.filemanip import md5, hash_infile, hash_timestamp
 from .traits_extension import (
     traits,
diff --git a/nipype/interfaces/base/tests/test_support.py b/nipype/interfaces/base/tests/test_support.py
index 52770e476c..406e6e9358 100644
--- a/nipype/interfaces/base/tests/test_support.py
+++ b/nipype/interfaces/base/tests/test_support.py
@@ -3,7 +3,7 @@
 import os
 import pytest
 
-from pkg_resources import resource_filename as pkgrf
+import acres
 
 from ....utils.filemanip import md5
 from ... import base as nib
@@ -42,14 +42,13 @@ def test_bunch_methods():
 def test_bunch_hash():
     # NOTE: Since the path to the json file is included in the Bunch,
     # the hash will be unique to each machine.
-    json_pth = pkgrf("nipype", os.path.join("testing", "data", "realign_json.json"))
+    json_pth = acres.Loader('nipype.testing').cached('data', 'realign_json.json')
 
-    b = nib.Bunch(infile=json_pth, otherthing="blue", yat=True)
+    b = nib.Bunch(infile=str(json_pth), otherthing="blue", yat=True)
     newbdict, bhash = b._get_bunch_hash()
     assert bhash == "d1f46750044c3de102efc847720fc35f"
     # Make sure the hash stored in the json file for `infile` is correct.
     jshash = md5()
-    with open(json_pth) as fp:
-        jshash.update(fp.read().encode("utf-8"))
+    jshash.update(json_pth.read_bytes())
     assert newbdict["infile"][0][1] == jshash.hexdigest()
     assert newbdict["yat"] is True
diff --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py
index ec19d1fe7b..1b9bdea6d5 100644
--- a/nipype/interfaces/dipy/base.py
+++ b/nipype/interfaces/dipy/base.py
@@ -2,6 +2,7 @@
 
 import os.path as op
 import inspect
+from functools import partial
 import numpy as np
 from ..base import (
     traits,
@@ -109,15 +110,15 @@ def convert_to_traits_type(dipy_type, is_file=False):
     dipy_type = dipy_type.lower()
     is_mandatory = bool("optional" not in dipy_type)
     if "variable" in dipy_type and "str" in dipy_type:
-        return traits.ListStr, is_mandatory
+        return partial(traits.List, traits.Str), is_mandatory
     elif "variable" in dipy_type and "int" in dipy_type:
-        return traits.ListInt, is_mandatory
+        return partial(traits.List, traits.Int), is_mandatory
     elif "variable" in dipy_type and "float" in dipy_type:
-        return traits.ListFloat, is_mandatory
+        return partial(traits.List, traits.Float), is_mandatory
     elif "variable" in dipy_type and "bool" in dipy_type:
-        return traits.ListBool, is_mandatory
+        return partial(traits.List, traits.Bool), is_mandatory
     elif "variable" in dipy_type and "complex" in dipy_type:
-        return traits.ListComplex, is_mandatory
+        return partial(traits.List, traits.Complex), is_mandatory
     elif "str" in dipy_type and not is_file:
         return traits.Str, is_mandatory
     elif "str" in dipy_type and is_file:
diff --git a/nipype/interfaces/dipy/tests/test_base.py b/nipype/interfaces/dipy/tests/test_base.py
index d2d81ec005..015215054d 100644
--- a/nipype/interfaces/dipy/tests/test_base.py
+++ b/nipype/interfaces/dipy/tests/test_base.py
@@ -16,7 +16,7 @@
 
 def test_convert_to_traits_type():
     Params = namedtuple("Params", "traits_type is_file")
-    Res = namedtuple("Res", "traits_type is_mandatory")
+    Res = namedtuple("Res", "traits_type subtype is_mandatory")
     l_entries = [
         Params("variable string", False),
         Params("variable int", False),
@@ -42,35 +42,38 @@ def test_convert_to_traits_type():
         Params("complex, optional", False),
     ]
     l_expected = [
-        Res(traits.ListStr, True),
-        Res(traits.ListInt, True),
-        Res(traits.ListFloat, True),
-        Res(traits.ListBool, True),
-        Res(traits.ListComplex, True),
-        Res(traits.ListInt, False),
-        Res(traits.ListStr, False),
-        Res(traits.ListFloat, False),
-        Res(traits.ListBool, False),
-        Res(traits.ListComplex, False),
-        Res(traits.Str, True),
-        Res(traits.Int, True),
-        Res(File, True),
-        Res(traits.Float, True),
-        Res(traits.Bool, True),
-        Res(traits.Complex, True),
-        Res(traits.Str, False),
-        Res(traits.Int, False),
-        Res(File, False),
-        Res(traits.Float, False),
-        Res(traits.Bool, False),
-        Res(traits.Complex, False),
+        Res(traits.List, traits.Str, True),
+        Res(traits.List, traits.Int, True),
+        Res(traits.List, traits.Float, True),
+        Res(traits.List, traits.Bool, True),
+        Res(traits.List, traits.Complex, True),
+        Res(traits.List, traits.Int, False),
+        Res(traits.List, traits.Str, False),
+        Res(traits.List, traits.Float, False),
+        Res(traits.List, traits.Bool, False),
+        Res(traits.List, traits.Complex, False),
+        Res(traits.Str, None, True),
+        Res(traits.Int, None, True),
+        Res(File, None, True),
+        Res(traits.Float, None, True),
+        Res(traits.Bool, None, True),
+        Res(traits.Complex, None, True),
+        Res(traits.Str, None, False),
+        Res(traits.Int, None, False),
+        Res(File, None, False),
+        Res(traits.Float, None, False),
+        Res(traits.Bool, None, False),
+        Res(traits.Complex, None, False),
     ]
 
     for entry, res in zip(l_entries, l_expected):
         traits_type, is_mandatory = convert_to_traits_type(
             entry.traits_type, entry.is_file
         )
-        assert traits_type == res.traits_type
+        trait_instance = traits_type()
+        assert isinstance(trait_instance, res.traits_type)
+        if res.subtype:
+            assert isinstance(trait_instance.inner_traits()[0].trait_type, res.subtype)
         assert is_mandatory == res.is_mandatory
 
     with pytest.raises(IOError):
diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py
index 09daacb17f..7dda9a49d7 100644
--- a/nipype/interfaces/fsl/epi.py
+++ b/nipype/interfaces/fsl/epi.py
@@ -417,7 +417,7 @@ def _generate_encfile(self):
                 float(val[0] == encdir[0]) * direction for val in ["x", "y", "z"]
             ] + [durations[idx]]
             lines.append(line)
-        np.savetxt(out_file, np.array(lines), fmt=b"%d %d %d %.8f")
+        np.savetxt(out_file, np.array(lines), fmt="%d %d %d %.8f")
         return out_file
 
     def _overload_extension(self, value, name=None):
diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py
index 2a148025f5..2ada4ab969 100644
--- a/nipype/interfaces/fsl/model.py
+++ b/nipype/interfaces/fsl/model.py
@@ -9,6 +9,7 @@
 from shutil import rmtree
 from string import Template
 
+import acres
 import numpy as np
 from looseversion import LooseVersion
 from nibabel import load
@@ -2547,12 +2548,5 @@ def load_template(name):
     template : string.Template
 
     """
-    from pkg_resources import resource_filename as pkgrf
-
-    full_fname = pkgrf(
-        "nipype", os.path.join("interfaces", "fsl", "model_templates", name)
-    )
-    with open(full_fname) as template_file:
-        template = Template(template_file.read())
-
-    return template
+    loader = acres.Loader('nipype.interfaces.fsl')
+    return Template(loader.readable('model_templates', name).read_text())
diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py
index 57cdad0168..0165087376 100644
--- a/nipype/interfaces/mrtrix3/preprocess.py
+++ b/nipype/interfaces/mrtrix3/preprocess.py
@@ -99,8 +99,9 @@ class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
         mandatory=True,
         desc="input DWI image",
     )
-    axes = traits.ListInt(
-        default_value=[0, 1],
+    axes = traits.List(
+        traits.Int,
+        [0, 1],
         usedefault=True,
         sep=",",
         minlen=2,
diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py
index cd15f36ac6..83f5bfef4b 100644
--- a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py
+++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py
@@ -9,8 +9,6 @@ def test_MRDeGibbs_inputs():
         ),
         axes=dict(
             argstr="-axes %s",
-            maxlen=2,
-            minlen=2,
             sep=",",
             usedefault=True,
         ),
diff --git a/nipype/interfaces/nilearn.py b/nipype/interfaces/nilearn.py
index 9d78517f79..df6413320e 100644
--- a/nipype/interfaces/nilearn.py
+++ b/nipype/interfaces/nilearn.py
@@ -105,7 +105,7 @@ def _run_interface(self, runtime):
 
         # save output
         self._results["out_file"] = os.path.join(runtime.cwd, self.inputs.out_file)
-        np.savetxt(self._results["out_file"], output, fmt=b"%s", delimiter="\t")
+        np.savetxt(self._results["out_file"], output, fmt="%s", delimiter="\t")
         return runtime
 
     def _process_inputs(self):
diff --git a/nipype/interfaces/nitime/tests/test_nitime.py b/nipype/interfaces/nitime/tests/test_nitime.py
index 64bb8366a0..8351a3c38a 100644
--- a/nipype/interfaces/nitime/tests/test_nitime.py
+++ b/nipype/interfaces/nitime/tests/test_nitime.py
@@ -51,7 +51,9 @@ def test_coherence_analysis(tmpdir):
 
     # This is the nitime analysis:
     TR = 1.89
-    data_rec = np.recfromcsv(example_data("fmri_timeseries.csv"))
+    data_rec = np.genfromtxt(
+        example_data("fmri_timeseries.csv"), delimiter=',', names=True
+    )
     roi_names = np.array(data_rec.dtype.names)
     n_samples = data_rec.shape[0]
     data = np.zeros((len(roi_names), n_samples))
diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py
index 8a3a479705..c7f69785ff 100644
--- a/nipype/interfaces/spm/preprocess.py
+++ b/nipype/interfaces/spm/preprocess.py
@@ -273,7 +273,8 @@ class ApplyVDMInputSpec(SPMCommandInputSpec):
         desc="phase encode direction input data have been acquired with",
         usedefault=True,
     )
-    write_which = traits.ListInt(
+    write_which = traits.List(
+        traits.Int,
         [2, 1],
         field="roptions.which",
         minlen=2,
@@ -524,7 +525,8 @@ class RealignInputSpec(SPMCommandInputSpec):
         field="eoptions.wrap",
         desc="Check if interpolation should wrap in [x,y,z]",
     )
-    write_which = traits.ListInt(
+    write_which = traits.List(
+        traits.Int,
         [2, 1],
         field="roptions.which",
         minlen=2,
@@ -731,7 +733,8 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec):
             "maximization and smoothness maximization of the estimated field."
         ),
     )
-    est_reg_factor = traits.ListInt(
+    est_reg_factor = traits.List(
+        traits.Int,
         [100000],
         field="uweoptions.lambda",
         minlen=1,
@@ -769,7 +772,8 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec):
         field="uweoptions.rem",
         desc="Re-estimate movement parameters at each unwarping iteration.",
     )
-    est_num_of_iterations = traits.ListInt(
+    est_num_of_iterations = traits.List(
+        traits.Int,
         [5],
         field="uweoptions.noi",
         minlen=1,
@@ -783,7 +787,8 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec):
         usedefault=True,
         desc="Point in position space to perform Taylor-expansion around.",
     )
-    reslice_which = traits.ListInt(
+    reslice_which = traits.List(
+        traits.Int,
         [2, 1],
         field="uwroptions.uwwhich",
         minlen=2,
diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyVDM.py b/nipype/interfaces/spm/tests/test_auto_ApplyVDM.py
index 2f56b49ef2..6d3b3c360d 100644
--- a/nipype/interfaces/spm/tests/test_auto_ApplyVDM.py
+++ b/nipype/interfaces/spm/tests/test_auto_ApplyVDM.py
@@ -41,8 +41,6 @@ def test_ApplyVDM_inputs():
         ),
         write_which=dict(
             field="roptions.which",
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         write_wrap=dict(
diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py
index 5165d6f33e..8262243a61 100644
--- a/nipype/interfaces/spm/tests/test_auto_Realign.py
+++ b/nipype/interfaces/spm/tests/test_auto_Realign.py
@@ -56,8 +56,6 @@ def test_Realign_inputs():
         ),
         write_which=dict(
             field="roptions.which",
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         write_wrap=dict(
diff --git a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py
index bb27419547..dc996c130e 100644
--- a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py
+++ b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py
@@ -15,8 +15,6 @@ def test_RealignUnwarp_inputs():
         ),
         est_num_of_iterations=dict(
             field="uweoptions.noi",
-            maxlen=1,
-            minlen=1,
             usedefault=True,
         ),
         est_re_est_mov_par=dict(
@@ -24,8 +22,6 @@ def test_RealignUnwarp_inputs():
         ),
         est_reg_factor=dict(
             field="uweoptions.lambda",
-            maxlen=1,
-            minlen=1,
             usedefault=True,
         ),
         est_reg_order=dict(
@@ -80,8 +76,6 @@ def test_RealignUnwarp_inputs():
         ),
         reslice_which=dict(
             field="uwroptions.uwwhich",
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         reslice_wrap=dict(
diff --git a/nipype/pipeline/engine/tests/test_engine.py b/nipype/pipeline/engine/tests/test_engine.py
index abf9426d43..f1b6817e74 100644
--- a/nipype/pipeline/engine/tests/test_engine.py
+++ b/nipype/pipeline/engine/tests/test_engine.py
@@ -541,7 +541,9 @@ def test_write_graph_dotfile(tmpdir, graph_type, simple):
     pipe.write_graph(graph2use=graph_type, simple_form=simple, format="dot")
 
     with open("graph.dot") as f:
-        graph_str = f.read()
+        # Replace handles change in networkx behavior when graph is missing a name
+        # Probably around 3, but I haven't tracked it down.
+        graph_str = f.read().replace('  {', ' {')
 
     if simple:
         for line in dotfiles[graph_type]:
@@ -635,7 +637,9 @@ def test_write_graph_dotfile_iterables(tmpdir, graph_type, simple):
     pipe.write_graph(graph2use=graph_type, simple_form=simple, format="dot")
 
     with open("graph.dot") as f:
-        graph_str = f.read()
+        # Replace handles change in networkx behavior when graph is missing a name
+        # Probably around 3, but I haven't tracked it down.
+        graph_str = f.read().replace('  {', ' {')
 
     if simple:
         for line in dotfiles_iter[graph_type]:
diff --git a/nipype/pipeline/plugins/tests/test_callback.py b/nipype/pipeline/plugins/tests/test_callback.py
index f7606708c7..b10238ec4a 100644
--- a/nipype/pipeline/plugins/tests/test_callback.py
+++ b/nipype/pipeline/plugins/tests/test_callback.py
@@ -1,8 +1,9 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Tests for workflow callbacks
-"""
+"""Tests for workflow callbacks."""
+from pathlib import Path
 from time import sleep
+import json
 import pytest
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
@@ -60,3 +61,51 @@ def test_callback_exception(tmpdir, plugin, stop_on_first_crash):
 
     sleep(0.5)  # Wait for callback to be called (python 2.7)
     assert so.statuses == [("f_node", "start"), ("f_node", "exception")]
+
+
+@pytest.mark.parametrize("plugin", ["Linear", "MultiProc", "LegacyMultiProc"])
+def test_callback_gantt(tmp_path: Path, plugin: str) -> None:
+    import logging
+
+    from os import path
+
+    from nipype.utils.profiler import log_nodes_cb
+    from nipype.utils.draw_gantt_chart import generate_gantt_chart
+
+    log_filename = tmp_path / "callback.log"
+    logger = logging.getLogger("callback")
+    logger.setLevel(logging.DEBUG)
+    handler = logging.FileHandler(log_filename)
+    logger.addHandler(handler)
+
+    # create workflow
+    wf = pe.Workflow(name="test", base_dir=str(tmp_path))
+    f_node = pe.Node(
+        niu.Function(function=func, input_names=[], output_names=[]), name="f_node"
+    )
+    wf.add_nodes([f_node])
+    wf.config["execution"] = {"crashdump_dir": wf.base_dir, "poll_sleep_duration": 2}
+
+    plugin_args = {"status_callback": log_nodes_cb}
+    if plugin != "Linear":
+        plugin_args["n_procs"] = 8
+    wf.run(plugin=plugin, plugin_args=plugin_args)
+
+    with open(log_filename, "r") as _f:
+        loglines = _f.readlines()
+
+    # test missing duration
+    first_line = json.loads(loglines[0])
+    if "duration" in first_line:
+        del first_line["duration"]
+    loglines[0] = f"{json.dumps(first_line)}\n"
+
+    # test duplicate timestamp warning
+    loglines.append(loglines[-1])
+
+    with open(log_filename, "w") as _f:
+        _f.write("".join(loglines))
+
+    with pytest.warns(Warning):
+        generate_gantt_chart(str(log_filename), 1 if plugin == "Linear" else 8)
+    assert (tmp_path / "callback.log.html").exists()
diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py
index 3ae4b77246..64a0d793db 100644
--- a/nipype/utils/draw_gantt_chart.py
+++ b/nipype/utils/draw_gantt_chart.py
@@ -8,8 +8,10 @@
 import random
 import datetime
 import simplejson as json
+from typing import Union
 
 from collections import OrderedDict
+from warnings import warn
 
 # Pandas
 try:
@@ -66,9 +68,9 @@ def create_event_dict(start_time, nodes_list):
         finish_delta = (node["finish"] - start_time).total_seconds()
 
         # Populate dictionary
-        if events.get(start_delta) or events.get(finish_delta):
+        if events.get(start_delta):
             err_msg = "Event logged twice or events started at exact same time!"
-            raise KeyError(err_msg)
+            warn(err_msg, category=Warning)
         events[start_delta] = start_node
         events[finish_delta] = finish_node
 
@@ -101,15 +103,25 @@ def log_to_dict(logfile):
 
     nodes_list = [json.loads(l) for l in lines]
 
-    def _convert_string_to_datetime(datestring):
-        try:
+    def _convert_string_to_datetime(
+        datestring: Union[str, datetime.datetime],
+    ) -> datetime.datetime:
+        """Convert a date string to a datetime object."""
+        if isinstance(datestring, datetime.datetime):
+            datetime_object = datestring
+        elif isinstance(datestring, str):
+            date_format = (
+                "%Y-%m-%dT%H:%M:%S.%f%z"
+                if "+" in datestring
+                else "%Y-%m-%dT%H:%M:%S.%f"
+            )
             datetime_object: datetime.datetime = datetime.datetime.strptime(
-                datestring, "%Y-%m-%dT%H:%M:%S.%f"
+                datestring, date_format
             )
-            return datetime_object
-        except Exception as _:
-            pass
-        return datestring
+        else:
+            msg = f"{datestring} is not a string or datetime object."
+            raise TypeError(msg)
+        return datetime_object
 
     date_object_node_list: list = list()
     for n in nodes_list:
@@ -154,12 +166,18 @@ def calculate_resource_timeseries(events, resource):
     # Iterate through the events
     for _, event in sorted(events.items()):
         if event["event"] == "start":
-            if resource in event and event[resource] != "Unknown":
-                all_res += float(event[resource])
+            if resource in event:
+                try:
+                    all_res += float(event[resource])
+                except ValueError:
+                    continue
             current_time = event["start"]
         elif event["event"] == "finish":
-            if resource in event and event[resource] != "Unknown":
-                all_res -= float(event[resource])
+            if resource in event:
+                try:
+                    all_res -= float(event[resource])
+                except ValueError:
+                    continue
             current_time = event["finish"]
         res[current_time] = all_res
 
@@ -284,7 +302,14 @@ def draw_nodes(start, nodes_list, cores, minute_scale, space_between_minutes, co
         # Left
         left = 60
         for core in range(len(end_times)):
-            if end_times[core] < node_start:
+            try:
+                end_time_condition = end_times[core] < node_start
+            except TypeError:
+                # if one has a timezone and one does not
+                end_time_condition = end_times[core].replace(
+                    tzinfo=None
+                ) < node_start.replace(tzinfo=None)
+            if end_time_condition:
                 left += core * 30
                 end_times[core] = datetime.datetime(
                     node_finish.year,
@@ -307,7 +332,7 @@ def draw_nodes(start, nodes_list, cores, minute_scale, space_between_minutes, co
             "offset": offset,
             "scale_duration": scale_duration,
             "color": color,
-            "node_name": node["name"],
+            "node_name": node.get("name", node.get("id", "")),
             "node_dur": node["duration"] / 60.0,
             "node_start": node_start.strftime("%Y-%m-%d %H:%M:%S"),
             "node_finish": node_finish.strftime("%Y-%m-%d %H:%M:%S"),
@@ -527,6 +552,25 @@ def generate_gantt_chart(
     # Read in json-log to get list of node dicts
     nodes_list = log_to_dict(logfile)
 
+    # Only include nodes with timing information, and convert timestamps
+    # from strings to datetimes
+    nodes_list = [
+        {
+            k: (
+                datetime.datetime.strptime(i[k], "%Y-%m-%dT%H:%M:%S.%f")
+                if k in {"start", "finish"} and isinstance(i[k], str)
+                else i[k]
+            )
+            for k in i
+        }
+        for i in nodes_list
+        if "start" in i and "finish" in i
+    ]
+
+    for node in nodes_list:
+        if "duration" not in node:
+            node["duration"] = (node["finish"] - node["start"]).total_seconds()
+
     # Create the header of the report with useful information
     start_node = nodes_list[0]
     last_node = nodes_list[-1]
diff --git a/pyproject.toml b/pyproject.toml
index 06f4d798c7..2b1282eb74 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,3 +4,24 @@ build-backend = "setuptools.build_meta"
 
 [tool.black]
 skip-string-normalization = true
+
+[tool.pytest.ini_options]
+minversion = "6"
+testpaths = ["nipype"]
+log_cli_level = "INFO"
+xfail_strict = true
+norecursedirs = [".git"]
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  "--cov=nipype",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
+doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
+env = "PYTHONHASHSEED=0"
+filterwarnings = ["ignore::DeprecationWarning"]
+junit_family = "xunit2"
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 0000000000..e8bc7e8f04
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,111 @@
+[tox]
+requires =
+  tox>=4
+envlist =
+  py3{9,10,11,12,13}-none # Test nipype functionality on all versions
+  py3{9,12,13}-full       # Test with extra dependencies on oldest and two newest
+  py39-min                # Test with minimal dependencies
+  py3{11,12,13}-pre       # Test with pre-release on SPEC0-supported Python
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.9: py39
+  3.10: py310
+  3.11: py311
+  3.12: py312
+  3.13: py313
+
+[gh-actions:env]
+DEPENDS =
+  min: min
+  none: none
+  full: full
+  pre: pre
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pip_pre =
+  pre: true
+pass_env =
+  # Parsed from `git grep getenv` and `git grep os.environ`
+  # May not all be needed
+  NIPYPE_NO_ET
+  NO_ET
+  ANTSPATH
+  CI_SKIP_TEST
+  FREESURFER_HOME
+  USER
+  FSLDIR
+  FSLOUTPUTTYPE
+  FSL_COURSE_DATA
+  NIPYPE_NO_MATLAB
+  OMP_NUM_THREADS
+  NIPYPE_NO_R
+  SPMMCRCMD
+  FORCE_SPMMCR
+  LOGNAME
+  AWS_ACCESS_KEY_ID
+  AWS_SECRET_ACCESS_KEY
+  MATLABCMD
+  MRTRIX3_HOME
+  RCMD
+  ETS_TOOLKIT
+  NIPYPE_CONFIG_DIR
+  DISPLAY
+  PATHEXT
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  PYTHON_GIL
+deps =
+  py313: traits @ git+https://github.com/enthought/traits.git@10954eb
+  full: dipy @ git+https://github.com/dipy/dipy@master
+extras =
+  tests
+  full: doc
+  full: profiler
+  full: duecredit
+  full: ssh
+  full: nipy
+setenv =
+  FSLOUTPUTTYPE=NIFTI_GZ
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+  pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+uv_resolution =
+  min: lowest-direct
+
+commands =
+  python -c "import nipype; print(nipype.__version__)"
+  pytest --durations=20 --durations-min=1.0 --cov-report term-missing {posargs:-n auto}
+
+[testenv:specs]
+description = Rebuild spec tests
+deps =
+  black
+  # Rebuild dipy specs
+  dipy
+  # Faster to install old numpy than unreleased Dipy
+  # This can be dropped once a Dipy release supports numpy 2
+  numpy<2
+commands =
+  python tools/checkspecs.py
+
+[testenv:style]
+description = Check our style guide
+labels = check
+deps =
+  black
+skip_install = true
+commands =
+  black --check --diff nipype setup.py