junifer 0.0.8.dev318__tar.gz → 0.0.8.dev326__tar.gz

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/.github/workflows/ci.yml

@@ -75,7 +75,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Set up uv
-        uses: astral-sh/setup-uv@v10.2.0
+        uses: astral-sh/setup-uv@v10.3.0
       - name: Install tox
         # tox-uv makes tox create the test environments with uv
         run: |
@@ -120,7 +120,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Set up uv
-        uses: astral-sh/setup-uv@v10.2.0
+        uses: astral-sh/setup-uv@v10.3.0
       - name: Install tox
         # tox-uv makes tox create the test environments with uv
         run: |

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/.github/workflows/docs-preview.yml

@@ -42,7 +42,7 @@ jobs:
         python-version: "3.12"
     - name: Set up uv
       if: github.event.action != 'closed' # The build is not needed when the preview is removed
-      uses: astral-sh/setup-uv@v10.2.0
+      uses: astral-sh/setup-uv@v10.3.0
     - name: Install Python dependencies
       if: github.event.action != 'closed' # The build is not needed when the preview is removed
       run: |

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/.github/workflows/docs.yml

@@ -32,7 +32,7 @@ jobs:
       with:
         python-version: "3.12"
     - name: Set up uv
-      uses: astral-sh/setup-uv@v10.2.0
+      uses: astral-sh/setup-uv@v10.3.0
     - name: Install Python dependencies
       run: |
         uv sync --locked --extra docs

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/.github/workflows/lint.yml

@@ -19,7 +19,7 @@ jobs:
         with:
           python-version: "3.x"
       - name: Set up uv
-        uses: astral-sh/setup-uv@v10.2.0
+        uses: astral-sh/setup-uv@v10.3.0
       - name: Install tox
         run: |
           uv tool install tox --with tox-uv

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/.github/workflows/publish.yml

@@ -27,7 +27,7 @@ jobs:
       with:
         python-version: "3.x"
     - name: Set up uv
-      uses: astral-sh/setup-uv@v10.2.0
+      uses: astral-sh/setup-uv@v10.3.0
     - name: Build package
       run:
         uv build

{junifer-0.0.8.dev318/junifer.egg-info → junifer-0.0.8.dev326}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev318
+Version: 0.0.8.dev326
 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>

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/docs/_static/css/custom.css

@@ -44,3 +44,26 @@ body:not([data-theme="light"]) .mermaid svg .marker{
   stroke: white !important;
   fill: white !important;
 }
+
+/* Use the full width of the page for the content (e.g., for wide tables):
+   Furo centers the content with a fixed width */
+.sidebar-drawer {
+  width: 15em;
+}
+
+/* The content takes the width left (not the width of its tables, which do not
+   wrap, and scroll instead), so the table of contents on the right is not
+   narrowed or moved out of the page */
+.main {
+  min-width: 0;
+}
+
+.content {
+  flex: 1 1 0;
+  min-width: 0;
+  width: auto;
+}
+
+.toc-drawer {
+  flex-shrink: 0;
+}

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/docs/builtin.rst

@@ -197,6 +197,14 @@ Marker
 Available
 ~~~~~~~~~
 
+The markers with a module in the *With* column need optional dependencies
+(e.g., ``neurokit2`` for ``junifer.markers.complexity``), so they are only
+available in the YAML file if their module is added to ``with``:
+
+.. code-block:: yaml
+
+  with: junifer.markers.complexity
+
 .. list-table::
    :widths: auto
    :header-rows: 1
@@ -205,123 +213,156 @@ Available
      - Description
      - State
      - Version Added
+     - With
    * - :class:`.ParcelAggregation`
      - Apply parcellation and perform aggregation function
      - Done
      - 0.0.1
+     -
    * - :class:`.SphereAggregation`
      - Spherical aggregation using mean
      - Done
      - 0.0.1
+     -
    * - :class:`.MapsAggregation`
      - Apply maps (probabilistic atlas) and extract mean time series per region
      - Done
      - 0.0.7
+     -
    * - :class:`.FunctionalConnectivityParcels`
      - Compute functional connectivity over parcellation
      - Done
      - 0.0.1
+     -
    * - :class:`.FunctionalConnectivitySpheres`
      - Compute functional connectivity over spheres placed on coordinates
      - Done
      - 0.0.1
+     -
    * - :class:`.FunctionalConnectivityMaps`
      - Compute functional connectivity over maps (probabilistic atlas)
      - Done
      - 0.0.7
+     -
    * - :class:`.CrossParcellationFC`
      - Compute functional connectivity across two parcellations
      - Done
      - 0.0.1
+     -
    * - :class:`.RSSETSMarker`
      - Compute root sum of squares of edgewise timeseries
      - Done
      - 0.0.1
+     -
    * - :class:`.ReHoParcels`
      - Calculate regional homogeneity over parcellation
      - Done
      - 0.0.1
+     -
    * - :class:`.ReHoSpheres`
      - Calculate regional homogeneity over spheres placed on coordinates
      - Done
      - 0.0.1
+     -
    * - :class:`.ReHoMaps`
      - Calculate regional homogeneity over maps (probabilistic atlas)
      - Done
      - 0.0.7
+     -
    * - :class:`.ALFFParcels`
      - Calculate (f)ALFF and aggregate using parcellations
      - Done
      - 0.0.1
+     -
    * - :class:`.ALFFSpheres`
      - Calculate (f)ALFF and aggregate using spheres placed on coordinates
      - Done
      - 0.0.1
+     -
    * - :class:`.ALFFMaps`
      - Calculate (f)ALFF and aggregate using maps (probabilistic atlas)
      - Done
      - 0.0.7
+     -
    * - :class:`.EdgeCentricFCParcels`
      - | Calculate edge-centric functional connectivity over parcellation, as
        | found in
        | `Jo et al. (2021) <https://doi.org/10.1016/j.neuroimage.2021.118204>`_
      - Done
      - 0.0.2
+     -
    * - :class:`.EdgeCentricFCSpheres`
      - | Calculate edge-centric functional connectivity over spheres placed on
        | coordinates, as found in
        | `Jo et al. (2021) <https://doi.org/10.1016/j.neuroimage.2021.118204>`_
      - Done
      - 0.0.2
+     -
    * - :class:`.EdgeCentricFCMaps`
      - | Calculate edge-centric functional connectivity over maps (probabilistic atlas),
        | as found in
        | `Jo et al. (2021) <https://doi.org/10.1016/j.neuroimage.2021.118204>`_
      - Done
      - 0.0.7
+     -
    * - :class:`.TemporalSNRParcels`
      - Calculate temporal signal-to-noise ratio using parcellations
      - Done
      - 0.0.2
+     -
    * - :class:`.TemporalSNRSpheres`
      - | Calculate temporal signal-to-noise ratio using spheres placed on
        | coordinates
      - Done
      - 0.0.2
+     -
    * - :class:`.TemporalSNRMaps`
      - Calculate temporal signal-to-noise ratio using maps (probabilistic atlas)
      - Done
      - 0.0.7
+     -
    * - :class:`.HurstExponent`
      - | Calculate Hurst exponent of a time series as found in
        | `Peng et al. (1995) <https://doi.org/10.1063/1.166141>`_
      - Done
      - 0.0.4
+     - ``junifer.markers.complexity``
    * - :class:`.MultiscaleEntropyAUC`
      - | Calculate AUC of multiscale entropy of a time series as found in
        | `Costa et al. (2002) <https://doi.org/10.1103/PhysRevLett.89.068102>`_
      - Done
      - 0.0.4
+     - ``junifer.markers.complexity``
    * - :class:`.PermEntropy`
      - | Calculate permutation entropy of a time series as found in
        | `Bandt at al. (2002) <https://doi.org/10.1103/PhysRevLett.88.174102>`_
      - Done
      - 0.0.4
+     - ``junifer.markers.complexity``
    * - :class:`.RangeEntropy`
      - | Calculate range entropy of a time series as found in
        | `Omidvarnia et al. (2018) <https://doi.org/10.3390/e20120962>`_
      - Done
      - 0.0.4
+     - ``junifer.markers.complexity``
    * - :class:`.RangeEntropyAUC`
      - | Calculate AUC of range entropy of a time series as found in
        | `Omidvarnia et al. (2018) <https://doi.org/10.3390/e20120962>`_
      - Done
      - 0.0.4
+     - ``junifer.markers.complexity``
    * - :class:`.SampleEntropy`
      - | Calculate sample entropy of a time series as found in
        | `Richman et al. (2000) <https://doi.org/10.1152/ajpheart.2000.278.6.H2039>`_
      - Done
      - 0.0.4
+     - ``junifer.markers.complexity``
+   * - :class:`.WeightedPermEntropy`
+     - | Calculate weighted permutation entropy of a time series as found in
+       | `Fadlallah et al. (2013) <https://doi.org/10.1103/PhysRevE.87.022911>`_
+     - Done
+     - 0.0.4
+     - ``junifer.markers.complexity``
 
 Planned
 ~~~~~~~

junifer-0.0.8.dev326/docs/changes/newsfragments/529.bugfix

@@ -0,0 +1 @@
+Fix the Maps markers (e.g., :class:`.MapsAggregation`) not being available in the YAML file without importing their modules by `Fede Raimondo`_

junifer-0.0.8.dev326/docs/changes/newsfragments/529.bugfix.1

@@ -0,0 +1 @@
+Fix the complexity markers (e.g., :class:`.HurstExponent`) not being available in the YAML file with ``with: junifer.markers.complexity`` by `Fede Raimondo`_

junifer-0.0.8.dev326/docs/changes/newsfragments/529.bugfix.2

@@ -0,0 +1 @@
+Fix ``junifer run`` and ``junifer list-elements`` ignoring the ``elements`` of the YAML file when ``--element`` is not given by `Fede Raimondo`_

junifer-0.0.8.dev326/docs/changes/newsfragments/529.bugfix.3

@@ -0,0 +1 @@
+Fix the AFNI smoothing of :class:`.Smoothing` leaving ``3dFWHMx.1D`` and ``3dFWHMx.1D.png`` in the current directory by `Fede Raimondo`_

junifer-0.0.8.dev326/docs/changes/newsfragments/529.doc

@@ -0,0 +1 @@
+Fix the ``collect_task`` option of the HTCondor queue being documented as ``collect``, document the ``elements`` key of the YAML file and the ``with`` needed by the markers, and use the full width of the page for the content by `Fede Raimondo`_

junifer-0.0.8.dev326/docs/changes/newsfragments/529.enh

@@ -0,0 +1 @@
+Add the ``cwd`` parameter to :func:`.run_ext_cmd` to run external commands in a directory by `Fede Raimondo`_

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/docs/using/queueing.rst

@@ -76,7 +76,7 @@ The following parameters are available for HTCondor:
   temporary directory.
 * ``extra_preamble``: Extra lines to be added to the HTCondor submit file. This
   can be used to add extra parameters to the job, such as ``requirements``.
-* ``collect``: This parameter allows to include a collect to the DAG to collect
+* ``collect_task``: This parameter allows to include a collect to the DAG to collect
   the results once all of the individual element jobs are finished. This is
   useful if you want to run a ``junifer collect`` job only once all of the
   individual element jobs are finished. Valid options are:
@@ -101,7 +101,7 @@ Example in YAML:
       shell: zsh
     mem: 8G
     disk: 2G
-    collect: "yes"  # wrap it in string to avoid boolean
+    collect_task: "yes"  # wrap it in string to avoid boolean
 
 Alternatively, if you use ``venv``, the YAML would look like so:
 
@@ -116,7 +116,7 @@ Alternatively, if you use ``venv``, the YAML would look like so:
       shell: zsh
     mem: 8G
     disk: 2G
-    collect: "yes"  # wrap it in string to avoid boolean
+    collect_task: "yes"  # wrap it in string to avoid boolean
 
 .. _queueing_local:
 

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/docs/using/running.rst

@@ -91,6 +91,16 @@ and then the ``elements.txt`` would be like so:
 
     sub-01
 
+The elements can also be set in the YAML file, with the ``elements`` key. They
+are used by ``run``, ``queue`` and ``list-elements`` when ``--element`` is not
+given (``--element`` has precedence over the YAML file):
+
+.. code-block:: yaml
+
+    elements:
+      - [sub-01, ses-01]
+      - [sub-02, ses-01]
+
 .. _running_elements:
 
 Complete and partial elements

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/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.dev318'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev318')
+__version__ = version = '0.0.8.dev326'
+__version_tuple__ = version_tuple = (0, 0, 8, 'dev326')
 
-__commit_id__ = commit_id = 'gd4a9dcd3a'
+__commit_id__ = commit_id = 'g1bcfcf0b5'

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/junifer/cli/parser.py

@@ -16,7 +16,7 @@ __all__ = ["parse_elements"]
 
 
 def parse_elements(element: tuple[str, ...], config: dict) -> Elements | None:
-    """Parse elements from cli.
+    """Parse elements from cli, or from the configuration if not in the cli.
 
     Parameters
     ----------
@@ -28,13 +28,13 @@ def parse_elements(element: tuple[str, ...], config: dict) -> Elements | None:
     Returns
     -------
     list or None
-        The element(s) as list or None.
+        The element(s) as list, or None (all the elements) if they are not in
+        the command-line options nor in the configuration.
 
     Raises
     ------
     ValueError
-        If no element is found either in the command-line options or
-        the configuration file.
+        If the ``elements`` key of the configuration has no value.
 
     Warns
     -----
@@ -44,9 +44,22 @@ def parse_elements(element: tuple[str, ...], config: dict) -> Elements | None:
 
     """
     logger.debug(f"Parsing elements: {element}")
-    # Early return None to continue with all elements
+    # Use the elements of the configuration if not in the command line
     if not element:
-        return None
+        if "elements" not in config:
+            # None to continue with all elements
+            return None
+        elements = config["elements"]
+        if elements is None:
+            raise_error(
+                "The `elements` key is set in the configuration, but its value"
+                " is `None`. It is likely that there is an empty `elements` "
+                "section in the yaml configuration file."
+            )
+        # A single element, and the elements with multiple values as tuples
+        if not isinstance(elements, list):
+            elements = [elements]
+        return [tuple(x) if isinstance(x, list) else x for x in elements]
     # Check if the element is a file for single element;
     # if yes, then parse elements from it
     if len(element) == 1 and Path(element[0]).resolve().is_file():
@@ -55,7 +68,7 @@ def parse_elements(element: tuple[str, ...], config: dict) -> Elements | None:
         # Process multi-keyed elements
         elements = [tuple(x.split(",")) if "," in x else x for x in element]
     logger.debug(f"Parsed elements: {elements}")
-    if elements is not None and "elements" in config:
+    if "elements" in config:
         warn_with_log(
             "One or more elements have been specified in both the command "
             "line and in the config file. The command line has precedence "
@@ -64,15 +77,6 @@ def parse_elements(element: tuple[str, ...], config: dict) -> Elements | None:
             "the configuration file will be ignored. To remove this warning, "
             "please remove the `elements` item from the configuration file."
         )
-    elif elements is None:
-        # Check in config
-        elements = config.get("elements", None)
-        if elements is None:
-            raise_error(
-                "The `elements` key is set in the configuration, but its value"
-                " is `None`. It is likely that there is an empty `elements` "
-                "section in the yaml configuration file."
-            )
     return elements
 
 

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/junifer/cli/tests/test_cli.py

@@ -22,7 +22,7 @@ from junifer.cli.cli import (
     selftest,
     wtf,
 )
-from junifer.cli.parser import _parse_elements_file
+from junifer.cli.parser import _parse_elements_file, parse_elements
 from junifer.pipeline import WorkDirManager
 
 
@@ -205,6 +205,47 @@ def test_multi_element_access(
     assert read_elements == expected_list
 
 
+@pytest.mark.parametrize(
+    "element, config, expected",
+    [
+        ((), {}, None),
+        ((), {"elements": ["sub-01", "sub-02"]}, ["sub-01", "sub-02"]),
+        ((), {"elements": "sub-01"}, ["sub-01"]),
+        ((), {"elements": [["sub-01", "ses-01"]]}, [("sub-01", "ses-01")]),
+        (("sub-01", "sub-02,ses-01"), {}, ["sub-01", ("sub-02", "ses-01")]),
+    ],
+)
+def test_parse_elements(
+    element: tuple[str, ...], config: dict, expected: list | None
+) -> None:
+    """Test parsing the elements from the command line or the configuration.
+
+    Parameters
+    ----------
+    element : tuple of str
+        The parametrized elements of the command line.
+    config : dict
+        The parametrized configuration.
+    expected : list or None
+        The parametrized elements to expect.
+
+    """
+    assert parse_elements(element, config) == expected
+
+
+def test_parse_elements_command_line_precedence() -> None:
+    """Test the elements of the command line have precedence."""
+    with pytest.warns(RuntimeWarning, match="command line has precedence"):
+        elements = parse_elements(("sub-01",), {"elements": ["sub-02"]})
+    assert elements == ["sub-01"]
+
+
+def test_parse_elements_empty_config() -> None:
+    """Test an empty elements key in the configuration."""
+    with pytest.raises(ValueError, match="its value is `None`"):
+        parse_elements((), {"elements": None})
+
+
 def test_queue(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
     """Test queue command.
 

junifer-0.0.8.dev326/junifer/markers/complexity/__init__.py

@@ -0,0 +1,38 @@
+"""Provide imports for complexity sub-package."""
+
+# Authors: Amir Omidvarnia <a.omidvarnia@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from importlib.util import find_spec
+
+from ..utils import raise_error
+
+
+# Check if neurokit2 is found
+if find_spec("neurokit2") is None:
+    raise_error(
+        msg="Could not find `neurokit2`, make sure the package is installed.",
+        klass=ImportError,
+    )
+
+# Not lazy: importing the sub-package (e.g., with ``with:`` in the YAML)
+# registers the markers, as they are not built-in components of the registry
+from .hurst_exponent import HurstExponent  # noqa: E402
+from .range_entropy import RangeEntropy  # noqa: E402
+from .range_entropy_auc import RangeEntropyAUC  # noqa: E402
+from .perm_entropy import PermEntropy  # noqa: E402
+from .weighted_perm_entropy import WeightedPermEntropy  # noqa: E402
+from .sample_entropy import SampleEntropy  # noqa: E402
+from .multiscale_entropy_auc import MultiscaleEntropyAUC  # noqa: E402
+
+
+__all__ = [
+    "HurstExponent",
+    "RangeEntropy",
+    "RangeEntropyAUC",
+    "PermEntropy",
+    "WeightedPermEntropy",
+    "SampleEntropy",
+    "MultiscaleEntropyAUC",
+]

junifer-0.0.8.dev326/junifer/markers/complexity/tests/test_complexity_registry.py

@@ -0,0 +1,48 @@
+"""Provide test for registering the complexity markers."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+# License: AGPL
+
+import subprocess
+import sys
+from pathlib import Path
+
+import pytest
+
+
+pytest.importorskip("neurokit2")
+
+
+def test_complexity_markers_with(tmp_path: Path) -> None:
+    """Test the complexity markers are registered with ``with:``.
+
+    It runs in a new Python process, so the markers are not registered by
+    other tests.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    names = [
+        "HurstExponent",
+        "MultiscaleEntropyAUC",
+        "PermEntropy",
+        "RangeEntropy",
+        "RangeEntropyAUC",
+        "SampleEntropy",
+        "WeightedPermEntropy",
+    ]
+    yaml_path = tmp_path / "config.yaml"
+    script = (
+        "from junifer.api.functions import parse_yaml\n"
+        "from junifer.pipeline import PipelineComponentRegistry\n"
+        "registry = PipelineComponentRegistry()\n"
+        f"assert 'HurstExponent' not in registry.step_components('marker')\n"
+        f"parse_yaml({str(yaml_path)!r})\n"
+        f"for name in {names!r}:\n"
+        "    registry.get_class('marker', name)\n"
+    )
+    yaml_path.write_text("with: junifer.markers.complexity\n")
+    subprocess.run([sys.executable, "-c", script], check=True)

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/junifer/pipeline/pipeline_component_registry.py

@@ -83,24 +83,30 @@ class PipelineComponentRegistry(metaclass=Singleton):
                 "TemporalFilter": "TemporalFilter",
             },
             "marker": {
+                "ALFFMaps": "ALFFMaps",
                 "ALFFParcels": "ALFFParcels",
                 "ALFFSpheres": "ALFFSpheres",
                 "BaseMarker": "BaseMarker",
                 "BrainPrint": "BrainPrint",
                 "CrossParcellationFC": "CrossParcellationFC",
+                "EdgeCentricFCMaps": "EdgeCentricFCMaps",
                 "EdgeCentricFCParcels": "EdgeCentricFCParcels",
                 "EdgeCentricFCSpheres": "EdgeCentricFCSpheres",
+                "FunctionalConnectivityMaps": "FunctionalConnectivityMaps",
                 "FunctionalConnectivityParcels": (
                     "FunctionalConnectivityParcels"
                 ),
                 "FunctionalConnectivitySpheres": (
                     "FunctionalConnectivitySpheres"
                 ),
+                "MapsAggregation": "MapsAggregation",
                 "ParcelAggregation": "ParcelAggregation",
+                "ReHoMaps": "ReHoMaps",
                 "ReHoParcels": "ReHoParcels",
                 "ReHoSpheres": "ReHoSpheres",
                 "RSSETSMarker": "RSSETSMarker",
                 "SphereAggregation": "SphereAggregation",
+                "TemporalSNRMaps": "TemporalSNRMaps",
                 "TemporalSNRParcels": "TemporalSNRParcels",
                 "TemporalSNRSpheres": "TemporalSNRSpheres",
             },

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/junifer/pipeline/tests/test_pipeline_component_registry.py

@@ -5,11 +5,14 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import importlib
 import logging
+import pkgutil
 from abc import ABC
 
 import pytest
 
+import junifer
 from junifer.datagrabber.pattern import PatternDataGrabber
 from junifer.pipeline.pipeline_component_registry import (
     PipelineComponentRegistry,
@@ -154,6 +157,42 @@ def test_pipeline_component_registry_get_class():
     assert isinstance(obj, type(bar))
 
 
+def test_pipeline_component_registry_get_class_builtin() -> None:
+    """Test get class for the built-in components of the registry."""
+    # A new registry, with the built-in components not imported yet (the
+    # singleton might have imported some of them)
+    registry = object.__new__(PipelineComponentRegistry)
+    registry.__init__()
+    for step in registry.steps:
+        for name in registry.step_components(step=step):
+            assert isinstance(registry.components[step][name], str)
+            klass = registry.get_class(step=step, name=name)
+            assert klass.__name__ == name
+    # Import all the components of the sub-packages of the steps, which
+    # registers them, and check that they are all built-in components, except
+    # the ones with optional dependencies, which are registered by importing
+    # their sub-package (e.g., with ``with:`` in the YAML)
+    optional = ("junifer.markers.complexity",)
+    for module in pkgutil.walk_packages(junifer.__path__, "junifer."):
+        if ".tests" in module.name:
+            continue
+        try:
+            importlib.import_module(module.name)
+        except ImportError:
+            # Only if the optional dependencies are not installed
+            assert module.name.startswith(optional)
+    for step, subpkg in registry._step_to_subpkg_mappings.items():
+        for name, klass in (
+            PipelineComponentRegistry().components[step].items()
+        ):
+            if isinstance(klass, str):
+                continue
+            if klass.__module__.startswith(optional):
+                assert name not in registry.components[step]
+            elif klass.__module__.startswith(f"junifer.{subpkg}."):
+                assert name in registry.components[step]
+
+
 def test_pipeline_component_registry_build():
     """Test component instance building for PipelineComponentRegistry."""
     import numpy as np

{junifer-0.0.8.dev318 → junifer-0.0.8.dev326}/junifer/preprocess/smoothing/_afni_smoothing.py

@@ -83,8 +83,9 @@ class AFNISmoothing:
             "-automask",
             f"-FWHM {fwhm}",
         ]
-        # Call 3dBlurToFWHM
-        run_ext_cmd(name="3dBlurToFWHM", cmd=blur_cmd)
+        # Call 3dBlurToFWHM, in the tempdir as it writes 3dFWHMx.1D and
+        # 3dFWHMx.1D.png in the current directory
+        run_ext_cmd(name="3dBlurToFWHM", cmd=blur_cmd, cwd=element_tempdir)
 
         # Read header to get output suffix
         header = input["data"].header