chore: Update minimum dependencies, test with tox-uv (#3412)

This is narrowly targeted to get tests passing.

Python 3.13 support depends on a new release of sdcflows. Will work on
that today.

Author: effigies

.github/workflows/contrib.yml

@@ -57,6 +57,8 @@ jobs:
         run: |
           sudo apt update
           sudo apt install -y --no-install-recommends graphviz
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
@@ -65,14 +67,32 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       - name: Install tox
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox tox-gh-actions
+          uv tool install --with=tox-uv --with=tox-gh-actions tox
       - name: Show tox config
         run: tox c
       - name: Run tox
         run: tox -v --exit-and-dump-after 1200
       - uses: codecov/codecov-action@v5
         with:
-          file: coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
+
+  checks:
+    runs-on: "ubuntu-latest"
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ["style", "spellcheck"]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+      - name: Install tox
+        run: uv tool install tox --with=tox-uv
+      - name: Show tox config
+        run: tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: tox -e ${{ matrix.check }}

.github/workflows/test.yml

@@ -38,7 +38,7 @@ def _aslist(inlist):
     aff_indexes = [
         ', '.join(
             [
-                '%d' % (affiliations.index(a) + 1)
+                str(affiliations.index(a) + 1)
                 for a in _aslist(author.get('affiliation', 'Unaffiliated'))
             ]
         )
@@ -52,7 +52,7 @@ def _aslist(inlist):
         file=sys.stderr,
     )
 
-    print('Authors (%d):' % len(author_matches))
+    print(f'Authors ({len(author_matches)}):')
     print(
         '{}.'.format(
             '; '.join(

.maint/paper_author_list.py

@@ -259,7 +259,7 @@ def _aslist(value):
     aff_indexes = [
         ', '.join(
             [
-                '%d' % (affiliations.index(a) + 1)
+                str(affiliations.index(a) + 1)
                 for a in _aslist(author.get('affiliation', 'Unaffiliated'))
             ]
         )
@@ -272,7 +272,7 @@ def _aslist(value):
             file=sys.stderr,
         )
 
-    print('Authors (%d):' % len(hits))
+    print(f'Authors ({len(hits)}):')
     print(
         '{}.'.format(
             '; '.join(

.maint/update_authors.py

@@ -82,9 +82,9 @@ def test_parser_valid(tmp_path, args):
         ('1000MB', 1),
         ('1T', 1000),
         ('1TB', 1000),
-        ('%dK' % 1e6, 1),
-        ('%dKB' % 1e6, 1),
-        ('%dB' % 1e9, 1),
+        ('1000000K', 1),
+        ('1000000KB', 1),
+        ('1000000000B', 1),
     ],
 )
 def test_memory_arg(tmp_path, argval, gb):

fmriprep/cli/tests/test_parser.py

@@ -149,11 +149,10 @@
     # Just get so analytics track one hit
     from contextlib import suppress
 
-    from requests import ConnectionError, ReadTimeout
-    from requests import get as _get_url
+    import requests
 
-    with suppress((ConnectionError, ReadTimeout)):
-        _get_url('https://rig.mit.edu/et/projects/nipy/nipype', timeout=0.05)
+    with suppress((requests.ConnectionError, requests.ReadTimeout)):
+        requests.get('https://rig.mit.edu/et/projects/nipy/nipype', timeout=0.05)
 
 # Execution environment
 _exec_env = os.name

fmriprep/config.py

@@ -26,6 +26,11 @@ def copytree_or_skip(source, target):
         pytest.skip(f'Cannot copy {data_dir!r} into {target / data_dir.name}. Probably in a zip.')
 
 
+@pytest.fixture(scope='session', autouse=True)
+def _legacy_printoptions():
+    np.set_printoptions(legacy='1.21')
+
+
 @pytest.fixture(autouse=True)
 def _populate_namespace(doctest_namespace, tmp_path):
     doctest_namespace['copytree_or_skip'] = copytree_or_skip

fmriprep/conftest.py

@@ -242,13 +242,13 @@ def _generate_segment(self):
         reg = {
             'FSL': [
                 'FSL <code>flirt</code> with boundary-based registration'
-                ' (BBR) metric - %d dof' % dof,
+                f' (BBR) metric - {dof} dof',
                 'FSL <code>flirt</code> rigid registration - 6 dof',
             ],
             'FreeSurfer': [
                 'FreeSurfer <code>bbregister</code> '
-                '(boundary-based registration, BBR) - %d dof' % dof,
-                'FreeSurfer <code>mri_coreg</code> - %d dof' % dof,
+                f'(boundary-based registration, BBR) - {dof} dof',
+                f'FreeSurfer <code>mri_coreg</code> - {dof} dof',
             ],
         }[self.inputs.registration][self.inputs.fallback]
 

fmriprep/interfaces/reports.py

@@ -116,7 +116,7 @@ def process_crashfile(crashfile):
                 scope.set_extra(k, strv[0])
             else:
                 for i, chunk in enumerate(strv):
-                    scope.set_extra('%s_%02d' % (k, i), chunk)
+                    scope.set_extra(f'{k}_{i:02d}', chunk)
 
         fingerprint = ''
         issue_title = f'{node_name}: {gist}'

fmriprep/utils/telemetry.py

@@ -106,7 +106,7 @@ def init_bold_stc_wf(
     frac = config.workflow.slice_time_ref
     tzero = np.round(first + frac * (last - first), 3)
 
-    afni_ver = ''.join('%02d' % v for v in afni.Info().version() or [])
+    afni_ver = ''.join(f'{v:02d}' for v in afni.Info().version() or [])
     workflow = Workflow(name=name)
     workflow.__desc__ = f"""\
 BOLD runs were slice-time corrected to {tzero:0.3g}s ({frac:g} of slice acquisition range

fmriprep/workflows/bold/stc.py

@@ -19,28 +19,28 @@ classifiers = [
 license = {file = "LICENSE"}
 requires-python = ">=3.10"
 dependencies = [
-    "acres",
-    "looseversion",
+    "acres >= 0.2.0",
+    "looseversion >= 1.3",
     "nibabel >= 4.0.1",
     "nipype >= 1.8.5",
-    "nireports >= 23.2.2",
-    "nitime",
-    "nitransforms >= 24.0.2",
-    "niworkflows >= 1.11.0",
-    "numpy >= 1.22",
-    "packaging",
-    "pandas",
+    "nireports >= 24.0.3",
+    "nitime >= 0.9",
+    "nitransforms >= 24.1.0",
+    "niworkflows >= 1.12.1",
+    "numpy >= 1.24",
+    "packaging >= 24",
+    "pandas >= 1.2",
     "psutil >= 5.4",
-    "pybids >= 0.15.2",
-    "requests",
+    "pybids >= 0.16",
+    "requests >= 2.27",
     "sdcflows >= 2.10.0",
     "smriprep >= 0.16.0",
     "tedana >= 23.0.2",
-    "templateflow >= 24.1.0",
-    "transforms3d",
-    "toml",
-    "codecarbon",
-    "APScheduler",
+    "templateflow >= 24.2.2",
+    "transforms3d >= 0.4",
+    "toml >= 0.10",
+    "codecarbon >= 2",
+    "APScheduler >= 3.10",
 ]
 dynamic = ["version"]
 
@@ -59,7 +59,7 @@ doc = [
     "sphinx_rtd_theme>=0.5.2",
 ]
 dev = [
-    "ruff ~= 0.4.3",
+    "ruff",
     "pre-commit",
 ]
 duecredit = ["duecredit"]
@@ -75,11 +75,11 @@ telemetry = [
     "sentry-sdk >= 1.3",
 ]
 test = [
-    "coverage[toml]",
-    "pytest",
-    "pytest-cov",
+    "coverage[toml] >= 5.2.1",
+    "pytest >= 8.1",
+    "pytest-cov >= 2.11",
     "pytest-env",
-    "pytest-xdist",
+    "pytest-xdist >= 2.5",
 ]
 maint = [
     "fuzzywuzzy",

pyproject.toml

@@ -38,21 +38,18 @@ pass_env =
   CLICOLOR
   CLICOLOR_FORCE
   PYTHON_GIL
+deps =
+  py313: traits @ git+https://github.com/enthought/traits.git@10954eb
 extras = test
 setenv =
+  pre: UV_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
   pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-deps =
-  min: nibabel == 4.0.1
-  min: nipype == 1.8.5
-  min: nitransforms == 21.0.0
-  min: numpy == 1.22
-  min: psutil == 5.4
-  min: pybids == 0.15.2
-  min: tedana == 23.0.2
-  min: templateflow == 24.1.0
+uv_resolution =
+  min: lowest-direct
 
 commands_pre =
-  python scripts/fetch_templates.py
+  # Use py* to disable for other environments
+  py3{10,11,12,13}: python scripts/fetch_templates.py
 commands =
   pytest --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto}