junifer 0.0.8.dev270__tar.gz → 0.0.8.dev282__tar.gz

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/.github/workflows/ci.yml

@@ -44,7 +44,7 @@ jobs:
   run-tests-external:
     needs: changes
     if: needs.changes.outputs.code == 'true' || github.event_name == 'workflow_dispatch'
-    runs-on: [self-hosted, linux, x64, data-v7]
+    runs-on: [self-hosted, linux, x64, data-v8]
     strategy:
       fail-fast: false
       matrix:
@@ -105,7 +105,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
     steps:
       - name: Checkout repository
         uses: actions/checkout@v7

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/.github/workflows/docs-preview.yml

@@ -15,7 +15,7 @@ concurrency:
 
 jobs:
   build-docs:
-    runs-on: [self-hosted, linux, x64, data-v7]
+    runs-on: [self-hosted, linux, x64, data-v8]
     permissions:
       # Needed for preview deploy
       pull-requests: write
@@ -29,7 +29,7 @@ jobs:
       if: github.event.action != 'closed' # The build is not needed when the preview is removed
       run: |
         which make git-annex jq
-        ls -d "$HOME"/junifer_data/v7
+        ls -d "$HOME"/junifer_data/* && cat "$HOME/junifer-data-version"
     - name: Checkout repository
       uses: actions/checkout@v7
       with:

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/.github/workflows/docs.yml

@@ -12,7 +12,7 @@ on:
 
 jobs:
   build-docs:
-    runs-on: [self-hosted, linux, x64, data-v7]
+    runs-on: [self-hosted, linux, x64, data-v8]
     steps:
     - name: Check ANTs
       run: |
@@ -20,7 +20,7 @@ jobs:
     - name: Check tooling
       run: |
         which make git-annex jq
-        ls -d "$HOME"/junifer_data/v7
+        ls -d "$HOME"/junifer_data/* && cat "$HOME/junifer-data-version"
     - name: Checkout repository
       uses: actions/checkout@v7
       with:

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/.gitignore

@@ -71,6 +71,7 @@ instance/
 # Sphinx documentation
 docs/_build/
 docs/auto_examples
+docs/sg_execution_times.rst
 docs/generated
 docs/make.bat
 

junifer-0.0.8.dev282/.python-version

@@ -0,0 +1 @@
+3.13

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/Dockerfile-ci

@@ -65,7 +65,7 @@ ENV FSLDIR=/opt/fsl \
     PATH="/opt/fsl/share/fsl/bin:$PATH"
 
 # --- Hosted tool cache, pre-populated (no downloads at job time) ---
-ARG PYTHON_VERSIONS="3.10 3.11 3.12 3.13 3.14"
+ARG PYTHON_VERSIONS="3.11 3.12 3.13 3.14"
 ARG UBUNTU_TAG=24.04
 ENV AGENT_TOOLSDIRECTORY=/opt/hostedtoolcache
 RUN set -eux; \

{junifer-0.0.8.dev270/junifer.egg-info → junifer-0.0.8.dev282}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev270
+Version: 0.0.8.dev282
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -19,45 +19,43 @@ Classifier: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
-Requires-Dist: click<8.2,>=8.1.3
-Requires-Dist: numpy<2.4.0,>=1.26.0
-Requires-Dist: scipy<1.17.0,>=1.10.0
-Requires-Dist: datalad<1.3.0,>=1.0.0
-Requires-Dist: pandas<2.4.0,>=2.0.0
-Requires-Dist: nibabel<5.4.0,>=5.2.0
+Requires-Dist: click<8.6,>=8.1.3
+Requires-Dist: numpy<2.5.0,>=1.26.0
+Requires-Dist: scipy<1.18.0,>=1.10.0
+Requires-Dist: datalad<1.8.0,>=1.0.0
+Requires-Dist: pandas<3.1.0,>=2.0.0
+Requires-Dist: nibabel<5.5.0,>=5.2.0
 Requires-Dist: nilearn<0.15,>=0.14.0
-Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
-Requires-Dist: ruamel.yaml<0.19,>=0.17
+Requires-Dist: sqlalchemy<2.2.0,>=2.0.25
+Requires-Dist: ruamel.yaml<0.20,>=0.17
 Requires-Dist: h5py>=3.10
-Requires-Dist: tqdm<4.68.0,>=4.66.1
-Requires-Dist: templateflow<25.0.0,>=23.0.0
+Requires-Dist: tqdm<4.71.0,>=4.66.1
+Requires-Dist: templateflow<26.0.0,>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0
-Requires-Dist: lazy_loader==0.4
-Requires-Dist: importlib_metadata; python_version < "3.11"
+Requires-Dist: lazy_loader<0.7,>=0.4
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
-Requires-Dist: junifer-data>=1.5.0
-Requires-Dist: structlog<26.0.0,>=25.0.0
+Requires-Dist: junifer-data>=1.6.1
+Requires-Dist: structlog<27.0.0,>=25.0.0
 Requires-Dist: pydantic>=2.11.4
 Requires-Dist: aenum<3.2.0,>=3.1.0
-Requires-Dist: typing_extensions<4.16.0,>=4.15.0; python_version < "3.12"
+Requires-Dist: typing_extensions<4.17.0,>=4.15.0; python_version < "3.12"
 Provides-Extra: all
-Requires-Dist: bctpy==0.6.0; extra == "all"
-Requires-Dist: neurokit2>=0.1.7; extra == "all"
+Requires-Dist: bctpy<0.7,>=0.6.0; extra == "all"
+Requires-Dist: neurokit2==0.2.12; extra == "all"
 Provides-Extra: bct
-Requires-Dist: bctpy==0.6.0; extra == "bct"
+Requires-Dist: bctpy<0.7,>=0.6.0; extra == "bct"
 Provides-Extra: onthefly
-Requires-Dist: bctpy==0.6.0; extra == "onthefly"
+Requires-Dist: bctpy<0.7,>=0.6.0; extra == "onthefly"
 Provides-Extra: neurokit2
-Requires-Dist: neurokit2>=0.1.7; extra == "neurokit2"
+Requires-Dist: neurokit2==0.2.12; extra == "neurokit2"
 Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
@@ -65,14 +63,14 @@ Requires-Dist: ruff; extra == "dev"
 Requires-Dist: towncrier; extra == "dev"
 Provides-Extra: sphinx
 Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "sphinx"
-Requires-Dist: sphinx<8.4.0,>=7.3.0; extra == "sphinx"
-Requires-Dist: sphinx-gallery<0.20.0,>=0.17.0; extra == "sphinx"
-Requires-Dist: furo<2025.10.0,>=2024.4.27; extra == "sphinx"
-Requires-Dist: numpydoc<=1.9.0,>=1.6.0; extra == "sphinx"
+Requires-Dist: sphinx<9.0.0,>=7.3.0; extra == "sphinx"
+Requires-Dist: sphinx-gallery<0.23.0,>=0.17.0; extra == "sphinx"
+Requires-Dist: furo<2026.0.0,>=2024.4.27; extra == "sphinx"
+Requires-Dist: numpydoc<1.12.0,>=1.6.0; extra == "sphinx"
 Requires-Dist: julearn==0.3.5; extra == "sphinx"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "sphinx"
-Requires-Dist: towncrier<=25.8.0,>=24.7.0; extra == "sphinx"
-Requires-Dist: sphinxcontrib-mermaid<=1.0.0,>=0.8.1; extra == "sphinx"
+Requires-Dist: towncrier<26.10.0,>=24.7.0; extra == "sphinx"
+Requires-Dist: sphinxcontrib-mermaid<2.2.0,>=0.8.1; extra == "sphinx"
 Requires-Dist: sphinxcontrib-towncrier==0.5.0a0; extra == "sphinx"
 Requires-Dist: setuptools-scm>=8; extra == "sphinx"
 Requires-Dist: autodoc_pydantic>=2.0.0; extra == "sphinx"

junifer-0.0.8.dev282/conda-env.yml

@@ -0,0 +1,53 @@
+name: junifer-dev
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.11,<=3.14
+  - click>=8.1.3,<8.6
+  - numpy>=1.26.0,<2.5.0
+  - scipy>=1.10.0,<1.18.0
+  - pandas>=2.0.0,<3.1.0
+  - nibabel>=5.2.0,<5.5.0
+  - nilearn>=0.14.0,<0.15
+  - sqlalchemy>=2.0.25,<2.2.0
+  - ruamel.yaml>=0.17,<0.20
+  - h5py>=3.10
+  - tqdm>=4.66.1,<4.71.0
+  - templateflow>=23.0.0,<26.0.0
+  - lapy>=1.0.0,<2.0.0
+  - lazy_loader>=0.4,<0.7
+  - looseversion==1.3.0
+  - bctpy>=0.6.0,<0.7
+  - neurokit2==0.2.12
+  - seaborn>=0.13.0,<0.14.0
+  # enum-tools fails with Sphinx 9 (domdfcoding/enum_tools#118, see
+  # juaml/junifer#519)
+  - sphinx>=7.3.0,<9.0.0
+  - sphinx-gallery>=0.17.0,<0.23.0
+  - furo>=2024.4.27,<2026.0.0
+  - numpydoc>=1.6.0,<1.12.0
+  - sphinx-copybutton>=0.5.1,<0.5.3
+  - towncrier>=24.7.0,<26.10.0
+  - sphinxcontrib-mermaid>=0.8.1,<2.2.0
+  - setuptools-scm>=8
+  - tox
+  - pre-commit
+  - ruff>=0.1.0
+  - ipykernel
+  - pytest-cov
+  - pytest
+  - codespell
+  - pip
+  - pip:
+    - datalad>=1.0.0,<1.8.0
+    - junifer-data>=1.6.1
+    - structlog>=25.0.0,<27.0.0
+    - pydantic>=2.11.4
+    - aenum>=3.1.0,<3.2.0
+    - typing_extensions>=4.15.0,<4.17.0
+    - julearn==0.3.5
+    - sphinxcontrib-towncrier==0.5.0a0
+    - autodoc_pydantic>=2.0.0
+    - enum-tools[sphinx]>=0.13.0,<0.14.0
+    - sphinx-polyversion>=2.0.0
+    - beautifulsoup4>=4.12.0

junifer-0.0.8.dev282/docs/changes/newsfragments/516.bugfix

@@ -0,0 +1 @@
+Keep the 2D output of :class:`.SphereAggregation`, :class:`.ParcelAggregation` and :class:`.MapsAggregation` for 3D images with ``nilearn`` 0.14 by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/516.bugfix.1

@@ -0,0 +1 @@
+Fix :class:`.JuniferConnectivityMeasure` not checking its input as ``nilearn``'s ``ConnectivityMeasure`` (e.g. tangent with a single subject) and not listing all the valid kinds in the error message by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/516.bugfix.2

@@ -0,0 +1 @@
+Fix ``dtype`` being ignored in :class:`.JuniferNiftiSpheresMasker` by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/516.change

@@ -0,0 +1 @@
+Replace boolean values of ``standardize`` in :class:`.TemporalFilter`, :class:`.fMRIPrepConfoundRemover` and :class:`.JuniferConnectivityMeasure` with ``"zscore_sample"`` (default), ``"psc"`` or ``None``, following ``nilearn``; booleans raise an error. ``"zscore_sample"`` uses the sample standard deviation, while ``True`` used the population one, so standardized values change slightly by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/516.change.1

@@ -0,0 +1 @@
+Use the BIDS version of the SPM auditory dataset in :class:`.SPMAuditoryTestingDataGrabber`, which has 84 timepoints instead of 96 by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/516.misc

@@ -0,0 +1 @@
+Support ``nilearn`` 0.14 (required) by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.bugfix

@@ -0,0 +1 @@
+Fix the labels of the ``Yan`` parcellations, which were ``NaN`` or numbers instead of the region names, which changes their feature names by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.bugfix.1

@@ -0,0 +1 @@
+Fix the labels of the ``Shen_2013`` parcellations, which were assigned to the wrong parcels, and add a ``-{i}`` suffix to the repeated ``No_BA_region`` labels, which changes their feature names by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.bugfix.2

@@ -0,0 +1 @@
+Fix the labels of the ``Brainnetome`` parcellations, which repeated each name for both hemispheres, by reading them from junifer-data (e.g. ``SFG_L_7_1`` and ``SFG_R_7_1`` instead of ``SFG_L(R)_7_1`` twice), which changes their feature names by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.bugfix.3

@@ -0,0 +1 @@
+Fix the labels of the ``Julich-Brain`` parcellations, which were the label values instead of the region names, which changes their feature names by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.bugfix.4

@@ -0,0 +1 @@
+Fix the labels of parcellations with regions lost when resampling or warping to the target image, which shifted the labels of the following regions; the lost regions are kept (without data) and a warning lists them by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.bugfix.5

@@ -0,0 +1 @@
+Fix :func:`.get_template` with ``templateflow`` 25 by only using resolutions that have the requested files, and choosing them by voxel size instead of resolution label by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.bugfix.6

@@ -0,0 +1 @@
+Fix updating existing rows in :class:`.SQLiteFeatureStorage` with ``pandas`` 3 by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.change

@@ -0,0 +1 @@
+Use :class:`enum.StrEnum` for the enumerations, so ``str()`` and formatting of their members give their value (e.g. ``"mean"``) instead of ``"AggFunc.Mean"`` by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.doc

@@ -0,0 +1 @@
+Fix the docs build and the julearn example, whose scores were ``NaN`` with ``scikit-learn`` 1.8 by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.misc

@@ -0,0 +1 @@
+Update the dependencies to their latest versions supporting Python 3.11 (e.g. ``numpy`` 2.4, ``pandas`` 3.0, ``scipy`` 1.17, ``click`` 8.5, ``datalad`` 1.7, ``templateflow`` 25), fixing the open security alerts, require ``junifer-data`` >= 1.6.1 and use junifer-data v8 by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.misc.1

@@ -0,0 +1 @@
+Pin ``neurokit2`` to 0.2.12, as 0.2.13 requires ``pandas`` < 3, and provide ``np.trapz`` (removed in ``numpy`` 2.4) while :class:`.MultiscaleEntropyAUC` calls ``neurokit2`` by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.misc.2

@@ -0,0 +1 @@
+Cap ``sphinx`` below 9, as ``enum-tools`` does not support it yet by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.misc.3

@@ -0,0 +1 @@
+Read dependency versions from the distribution metadata instead of the deprecated ``__version__`` attributes, pass ``standardize=None`` to ``nilearn`` maskers to avoid deprecation warnings and skip the tests of vendored packages with a ``pytest_ignore_collect`` hook, as ``datalad``'s pytest plugin prevents ``collect_ignore`` from being applied by `Fede Raimondo`_

junifer-0.0.8.dev282/docs/changes/newsfragments/520.removal

@@ -0,0 +1 @@
+Drop support for Python 3.10 by `Fede Raimondo`_

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/docs/conf.py

@@ -85,6 +85,7 @@ nitpick_ignore_regex = [
     ("py:obj", "them"),  # ignore them
     ("py:class", "junifer.utils.helpers.ensure_list"),  # ignore ensure_list
     ("py:class", "junifer.utils.helpers.ensure_list_or_none"),  # ignore ensure_list_or_none
+    ("py:class", "junifer.utils.helpers.check_standardize"),  # ignore check_standardize
     # Unresolved names in source annotations, e.g. ``types`` of
     # PatternDataladDataGrabber when building with sphinx-polyversion
     ("py:class", "BeforeValidator"),

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/examples/run_junifer_julearn.py

@@ -109,8 +109,9 @@ scores = run_cross_validation(
     data=df_vbm,
     model=creator,
     cv=3,
+    scoring="r2",
 )
-print(scores)
+print(scores[["fold", "test_score"]])
 
 ###############################################################################
 # Interpretation of results:

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8.dev270'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev270')
+__version__ = version = '0.0.8.dev282'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev282')
 
-__commit_id__ = commit_id = 'gcf60784bf'
+__commit_id__ = commit_id = 'g6eb25f9aa'

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/api/queue_context/htcondor_adapter.py

@@ -5,7 +5,7 @@
 
 import shutil
 import textwrap
-from enum import Enum
+from enum import StrEnum
 from pathlib import Path
 from typing import Any
 
@@ -23,7 +23,7 @@ from .queue_context_adapter import (
 __all__ = ["HTCondorAdapter", "HTCondorCollect"]
 
 
-class HTCondorCollect(str, Enum):
+class HTCondorCollect(StrEnum):
     """Accepted HTCondor collect commands.
 
     * ``"yes"``: Submit "collect" task and run even if some of the jobs

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/api/queue_context/queue_context_adapter.py

@@ -11,13 +11,9 @@ if sys.version_info < (3, 12):  # pragma: no cover
 else:
     from typing import TypedDict
 
-if sys.version_info < (3, 11):  # pragma: no cover
-    from typing_extensions import Required
-else:
-    from typing import Required
-
 from abc import ABC, abstractmethod
-from enum import Enum
+from enum import StrEnum
+from typing import Required
 
 import structlog
 from pydantic import BaseModel, ConfigDict
@@ -31,7 +27,7 @@ _log = structlog.get_logger("junifer")
 logger = _log.bind(pkg="api")
 
 
-class EnvKind(str, Enum):
+class EnvKind(StrEnum):
     """Accepted Python environment kind."""
 
     Venv = "venv"
@@ -39,7 +35,7 @@ class EnvKind(str, Enum):
     Local = "local"
 
 
-class EnvShell(str, Enum):
+class EnvShell(StrEnum):
     """Accepted environment shell."""
 
     Bash = "bash"

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/cli/__init__.py

@@ -3,17 +3,11 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import sys
+from importlib.metadata import entry_points
 
 import lazy_loader as lazy
 
 
-if sys.version_info < (3, 11):  # pragma: no cover
-    from importlib_metadata import entry_points
-else:
-    from importlib.metadata import entry_points
-
-
 __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
 
 

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/cli/tests/test_cli_utils.py

@@ -5,7 +5,6 @@
 
 import importlib
 import platform as pl
-import sys
 
 import pytest
 
@@ -56,9 +55,6 @@ def test_get_dependency_information_short() -> None:
         "typing_extensions",
     ]
 
-    if sys.version_info < (3, 11):
-        dependency_list.append("importlib_metadata")
-
     # Import dependencies as only loaded modules are reported
     for module in dependency_list:
         importlib.import_module(module)

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -5,7 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from enum import Enum
+from enum import StrEnum
 from typing import Annotated, ClassVar, Literal
 
 from pydantic import AnyUrl, BeforeValidator
@@ -19,7 +19,7 @@ from ....utils import ensure_list
 __all__ = ["IXISite", "JuselessDataladIXIVBM"]
 
 
-class IXISite(str, Enum):
+class IXISite(StrEnum):
     """Accepted IXI sites."""
 
     Guys = "Guys"

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/configs/juseless/datagrabbers/ucla.py

@@ -4,7 +4,7 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from enum import Enum
+from enum import StrEnum
 from pathlib import Path
 from typing import Annotated, Literal
 
@@ -19,7 +19,7 @@ from ....utils import ensure_list
 __all__ = ["JuselessUCLA", "UCLATask"]
 
 
-class UCLATask(str, Enum):
+class UCLATask(StrEnum):
     """Accepted UCLA tasks."""
 
     REST = "rest"

{junifer-0.0.8.dev270 → junifer-0.0.8.dev282}/junifer/conftest.py

@@ -5,15 +5,44 @@
 # License: AGPL
 
 import gc
+from pathlib import Path
 
 import pytest
 
 from junifer.utils.singleton import Singleton
 
 
-# Do not collect the tests of vendored packages. Paths are relative to this
-# file, so it also works when testing the installed package.
-collect_ignore = ["external/h5io", "external/BrainPrint"]
+# Vendored packages, whose tests are not collected. Paths are relative to
+# this file, so it also works when testing the installed package.
+_VENDORED = [
+    Path(__file__).parent / "external" / "h5io",
+    Path(__file__).parent / "external" / "BrainPrint",
+]
+
+
+# TODO: replace with ``collect_ignore`` once datalad/datalad#7967 is fixed
+# (see juaml/junifer#518)
+def pytest_ignore_collect(collection_path: Path) -> bool | None:
+    """Do not collect the tests of vendored packages.
+
+    This replaces ``collect_ignore``, which is not applied when datalad's
+    pytest plugin (datalad >= 1.4) is installed: its ``pytest_ignore_collect``
+    returns False for directories, so pytest's own check is never called.
+
+    Parameters
+    ----------
+    collection_path : pathlib.Path
+        The path being considered for collection.
+
+    Returns
+    -------
+    bool or None
+        True to ignore the path, None to let other hooks decide.
+
+    """
+    if any(collection_path.is_relative_to(path) for path in _VENDORED):
+        return True
+    return None
 
 
 def pytest_collection_finish(session: pytest.Session) -> None: