Merge pull request #3699 from effigies/fix/deprecations

FIX: Address numpy and traits deprecations

Author: effigies

Diff for: .github/workflows/contrib.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
@@ -82,70 +72,51 @@ 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' }}
-      - uses: codecov/codecov-action@v5
+          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:
           token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
@@ -159,7 +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
@@ -170,3 +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 for: .github/workflows/tests.yml

@@ -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 for: nipype/algorithms/confounds.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 for: nipype/algorithms/rapidart.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 for: nipype/algorithms/tests/test_auto_ArtifactDetect.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"""