Merge branch 'main' into gkm

aslprep/workflows/asl/outputs.py

@@ -659,9 +659,11 @@ def init_ds_volumes_wf(
     )
     workflow.connect([
         (inputnode, raw_sources, [("source_files", "in_files")]),
+        # Note that ANTs expects transforms in target-to-source order
+        # Reverse this for nitransforms-based resamplers
         (inputnode, aslref2target, [
-            ("aslref2anat_xfm", "in1"),
-            ("anat2std_xfm", "in2"),
+            ("anat2std_xfm", "in1"),
+            ("aslref2anat_xfm", "in2"),
         ]),
         (inputnode, ds_asl, [
             ("source_files", "source_file"),

docs/api.rst

@@ -12,88 +12,14 @@ Internal configuration system
    :members: from_dict, load, get, dumps, to_filename, init_spaces
 
 
-***********************************
-:mod:`aslprep.workflows`: Workflows
-***********************************
+***********
+Library API
+***********
 
-.. currentmodule:: aslprep
+.. toctree::
+   :glob:
 
-.. autosummary::
-   :toctree: generated/
-   :template: function.rst
-
-   aslprep.workflows.base
-   aslprep.workflows.asl.apply
-   aslprep.workflows.asl.base
-   aslprep.workflows.asl.cbf
-   aslprep.workflows.asl.confounds
-   aslprep.workflows.asl.fit
-   aslprep.workflows.asl.hmc
-   aslprep.workflows.asl.outputs
-   aslprep.workflows.asl.plotting
-   aslprep.workflows.asl.reference
-
-
-*************************************
-:mod:`aslprep.interfaces`: Interfaces
-*************************************
-
-.. automodule:: aslprep.interfaces
-   :no-members:
-   :no-inherited-members:
-
-.. currentmodule:: aslprep
-
-.. autosummary::
-   :toctree: generated/
-   :template: module.rst
-
-   aslprep.interfaces.ants
-   aslprep.interfaces.bids
-   aslprep.interfaces.cbf
-   aslprep.interfaces.confounds
-   aslprep.interfaces.parcellation
-   aslprep.interfaces.plotting
-   aslprep.interfaces.reference
-   aslprep.interfaces.reports
-   aslprep.interfaces.utility
-
-
-*******************************
-:mod:`aslprep.utils`: Utilities
-*******************************
-
-.. automodule:: aslprep.utils
-   :no-members:
-   :no-inherited-members:
-
-.. currentmodule:: aslprep
-
-.. autosummary::
-   :toctree: generated/
-   :template: module.rst
-
-   aslprep.utils.asl
-   aslprep.utils.atlas
-   aslprep.utils.bids
-   aslprep.utils.cbf
-   aslprep.utils.confounds
-   aslprep.utils.misc
-   aslprep.utils.plotting
-   aslprep.utils.sentry
-
-***********************************
-:mod:`aslprep.data`: Data resources
-***********************************
-
-.. automodule:: aslprep.data
-   :no-members:
-   :no-inherited-members:
-
-.. currentmodule:: aslprep
-
-.. autosummary::
-   :toctree: generated/
-   :template: module.rst
-
-   aslprep.data
+   api/aslprep.cli
+   api/aslprep.workflows
+   api/aslprep.interfaces
+   api/aslprep.utils

docs/conf.py

@@ -47,13 +47,10 @@
 # Add any Sphinx extension module names here, as strings.
 # They can be extensions coming with Sphinx (named "sphinx.ext.*") or your custom ones.
 extensions = [
-    "nbsphinx",
     "nipype.sphinxext.apidoc",
     "nipype.sphinxext.plot_workflow",
     "recommonmark",
     "sphinx.ext.autodoc",
-    "sphinx.ext.autosectionlabel",
-    "sphinx.ext.autosummary",  # standard
     "sphinx.ext.coverage",
     "sphinx.ext.doctest",
     "sphinx.ext.intersphinx",

pyproject.toml

@@ -18,25 +18,25 @@ license = {file = "LICENSE.md"}
 requires-python = ">=3.10"
 dependencies = [
     'importlib_resources; python_version < "3.11"',
-    "fmriprep ~= 23.2.0",
-    "indexed_gzip >= 0.8.8",
+    "fmriprep >= 23.2, <= 24.0",
+    "indexed_gzip <= 1.8",
     "looseversion",
     "networkx ~= 3.3",  # nipype needs networkx, but 3+ isn"t compatible with nipype 1.8.5
-    "nibabel >= 4.0.1",
+    "nibabel <= 5.1",
     "nilearn ~= 0.10.3",
     "nipype >= 1.8.5",
     "nitransforms >= 21.0.0",
     "niworkflows ~= 1.10.0",
-    "numpy >= 1.22",
+    "numpy >= 1.26",
     "packaging",
     "pandas",
-    "psutil >= 5.4",
-    "pybids ~= 0.16.4",
+    "psutil <= 5.9",
+    "pybids <= 0.16.4",
     "requests",
-    "sdcflows ~= 2.8.0",
-    "sentry-sdk >= 0.6.9",
-    "smriprep ~= 0.15.0",
-    "templateflow >= 23.0.0",
+    "sdcflows <= 2.8.1",
+    "sentry-sdk <= 1.45.0",
+    "smriprep <= 0.15",
+    "templateflow <= 23.0.0",
     "toml",
 ]
 dynamic = ["version"]