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Commit 5dc8701

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Merge pull request #3699 from effigies/fix/deprecations
FIX: Address numpy and traits deprecations
2 parents 1ccee34 + ddb73ac commit 5dc8701

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27 files changed

+299
-259
lines changed

27 files changed

+299
-259
lines changed

‎.github/workflows/contrib.yml‎

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This file was deleted.

‎.github/workflows/tests.yml‎

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@@ -1,22 +1,11 @@
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name: Stable tests
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# This file tests the claimed support range of nipype including
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#
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# * Operating systems: Linux, OSX
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# * Dependencies: minimum requirements, optional requirements
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# * Installation methods: setup.py, sdist, wheel, archive
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name: Tox
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on:
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push:
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branches:
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- master
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- maint/*
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tags:
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- "*"
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branches: [ master, main, 'maint/*' ]
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tags: [ '*' ]
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pull_request:
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branches:
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- master
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- maint/*
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branches: [ master, main, 'maint/*' ]
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schedule:
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# 8am EST / 9am EDT Mondays
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- cron: "0 13 * * 1"
@@ -26,27 +15,28 @@ defaults:
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shell: bash
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concurrency:
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group: tests-${{ github.ref }}
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions: {}
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permissions:
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contents: read
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env:
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# Force tox and pytest to use color
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FORCE_COLOR: true
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jobs:
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build:
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permissions:
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contents: read # to fetch code (actions/checkout)
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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with:
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python-version: 3
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- run: pip install --upgrade build twine
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- name: Build sdist and wheel
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run: python -m build
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- run: twine check dist/*
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v3
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- run: uv build
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- run: uvx twine check dist/*
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- uses: actions/upload-artifact@v4
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with:
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name: dist
@@ -82,70 +72,51 @@ jobs:
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- name: Run tests
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run: pytest --doctest-modules -v --pyargs nipype
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stable:
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test:
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# Check each OS, all supported Python, minimum versions and latest releases
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permissions:
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contents: read # to fetch code (actions/checkout)
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ["ubuntu-22.04"]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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check: ["test"]
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pip-flags: [""]
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depends: ["REQUIREMENTS"]
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deb-depends: [false]
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nipype-extras: ["doc,tests,profiler"]
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os: ["ubuntu-latest"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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dependencies: [none, full, pre]
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include:
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- os: ubuntu-22.04
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- os: ubuntu-latest
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python-version: "3.9"
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check: test
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pip-flags: ""
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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,profiler,duecredit,ssh
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- os: ubuntu-20.04
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python-version: "3.9"
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check: test
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pip-flags: ""
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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
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dependencies: min
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exclude:
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# Skip some intermediate versions for full tests
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- python-version: "3.10"
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dependencies: full
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- python-version: "3.11"
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dependencies: full
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# Do not test pre-releases for versions out of SPEC0
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- python-version: "3.9"
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dependencies: pre
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- python-version: "3.10"
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dependencies: pre
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env:
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DEPENDS: ${{ matrix.depends }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
120-
NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
121-
INSTALL_TYPE: pip
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CI_SKIP_TEST: 1
100+
DEPENDS: ${{ matrix.dependencies }}
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steps:
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- uses: actions/checkout@v4
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v3
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- name: Set up Python ${{ matrix.python-version }}
127107
uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
133-
run: tools/ci/create_venv.sh
134-
- name: Build archive
112+
- name: Install tox
135113
run: |
136-
source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
138-
- name: Install Debian dependencies
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run: tools/ci/install_deb_dependencies.sh
140-
if: ${{ matrix.os == 'ubuntu-latest' }}
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- name: Install dependencies
142-
run: tools/ci/install_dependencies.sh
143-
- name: Install Nipype
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run: tools/ci/install.sh
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- name: Run tests
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run: tools/ci/check.sh
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if: ${{ matrix.check != 'skiptests' }}
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- uses: codecov/codecov-action@v5
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uv tool install tox --with=tox-uv --with=tox-gh-actions
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- name: Show tox config
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run: tox c
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- name: Run tox
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run: tox -v --exit-and-dump-after 1200
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- uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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if: ${{ always() }}
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publish:
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runs-on: ubuntu-latest
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environment: "Package deployment"
162-
needs: [stable, test-package]
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needs: [test, test-package]
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
164135
steps:
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- uses: actions/download-artifact@v4
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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checks:
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runs-on: 'ubuntu-latest'
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continue-on-error: true
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strategy:
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matrix:
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check: ['specs', 'style']
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steps:
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- uses: actions/checkout@v4
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v3
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- name: Show tox config
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run: uvx tox c
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- name: Show tox config (this call)
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run: uvx tox c -e ${{ matrix.check }}
160+
- name: Run check
161+
run: uvx tox -e ${{ matrix.check }}

‎nipype/algorithms/confounds.py‎

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Original file line numberDiff line numberDiff line change
@@ -188,7 +188,7 @@ def _run_interface(self, runtime):
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189189
if self.inputs.save_std:
190190
out_file = self._gen_fname("dvars_std", ext="tsv")
191-
np.savetxt(out_file, dvars[0], fmt=b"%0.6f")
191+
np.savetxt(out_file, dvars[0], fmt="%0.6f")
192192
self._results["out_std"] = out_file
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194194
if self.inputs.save_plot:
@@ -228,7 +228,7 @@ def _run_interface(self, runtime):
228228

229229
if self.inputs.save_vxstd:
230230
out_file = self._gen_fname("dvars_vxstd", ext="tsv")
231-
np.savetxt(out_file, dvars[2], fmt=b"%0.6f")
231+
np.savetxt(out_file, dvars[2], fmt="%0.6f")
232232
self._results["out_vxstd"] = out_file
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234234
if self.inputs.save_plot:
@@ -251,8 +251,8 @@ def _run_interface(self, runtime):
251251
np.savetxt(
252252
out_file,
253253
np.vstack(dvars).T,
254-
fmt=b"%0.8f",
255-
delimiter=b"\t",
254+
fmt="%0.8f",
255+
delimiter="\t",
256256
header="std DVARS\tnon-std DVARS\tvx-wise std DVARS",
257257
comments="",
258258
)
@@ -689,7 +689,7 @@ def _run_interface(self, runtime):
689689
np.savetxt(
690690
components_file,
691691
components,
692-
fmt=b"%.10f",
692+
fmt="%.10f",
693693
delimiter="\t",
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header="\t".join(components_header),
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comments="",
@@ -729,7 +729,7 @@ def _run_interface(self, runtime):
729729
np.savetxt(
730730
self._results["pre_filter_file"],
731731
filter_basis,
732-
fmt=b"%.10f",
732+
fmt="%.10f",
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delimiter="\t",
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header="\t".join(header),
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comments="",

‎nipype/algorithms/rapidart.py‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -189,7 +189,8 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
189189
desc="Source of movement parameters",
190190
mandatory=True,
191191
)
192-
use_differences = traits.ListBool(
192+
use_differences = traits.List(
193+
traits.Bool,
193194
[True, False],
194195
minlen=2,
195196
maxlen=2,
@@ -600,10 +601,10 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
600601
outliers = np.unique(np.union1d(iidx, np.union1d(tidx, ridx)))
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602603
# write output to outputfile
603-
np.savetxt(artifactfile, outliers, fmt=b"%d", delimiter=" ")
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np.savetxt(intensityfile, g, fmt=b"%.2f", delimiter=" ")
604+
np.savetxt(artifactfile, outliers, fmt="%d", delimiter=" ")
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np.savetxt(intensityfile, g, fmt="%.2f", delimiter=" ")
605606
if self.inputs.use_norm:
606-
np.savetxt(normfile, normval, fmt=b"%.4f", delimiter=" ")
607+
np.savetxt(normfile, normval, fmt="%.4f", delimiter=" ")
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608609
if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
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import matplotlib

‎nipype/algorithms/tests/test_auto_ArtifactDetect.py‎

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@@ -48,8 +48,6 @@ def test_ArtifactDetect_inputs():
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xor=["norm_threshold"],
4949
),
5050
use_differences=dict(
51-
maxlen=2,
52-
minlen=2,
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usedefault=True,
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),
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use_norm=dict(

‎nipype/conftest.py‎

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
import shutil
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from tempfile import mkdtemp
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import pytest
5-
import numpy
5+
import numpyasnp
66
import py.path as pp
77

88
NIPYPE_DATADIR = os.path.realpath(
@@ -15,12 +15,17 @@
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1616
@pytest.fixture(autouse=True)
1717
def add_np(doctest_namespace):
18-
doctest_namespace["np"] = numpy
18+
doctest_namespace["np"] = np
1919
doctest_namespace["os"] = os
2020
doctest_namespace["pytest"] = pytest
2121
doctest_namespace["datadir"] = data_dir
2222

2323

24+
@pytest.fixture(scope='session', autouse=True)
25+
def legacy_printoptions():
26+
np.set_printoptions(legacy='1.21')
27+
28+
2429
@pytest.fixture(autouse=True)
2530
def _docdir(request):
2631
"""Grabbed from https://stackoverflow.com/a/46991331"""

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