From 0931fda459f5feb4dad74a31f5d622c8a4cc20d4 Mon Sep 17 00:00:00 2001
From: manuegrx <47973414+manuegrx@users.noreply.github.com>
Date: Tue, 10 Oct 2023 09:57:34 +0200
Subject: [PATCH 01/26] [fix] MRTrix3 change inputs position for MRTransform

---
 nipype/interfaces/mrtrix3/utils.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index 2ec7eba909..6909f380be 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -822,13 +822,11 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec):
     )
     invert = traits.Bool(
         argstr="-inverse",
-        position=1,
         desc="Invert the specified transform before using it",
     )
     linear_transform = File(
         exists=True,
         argstr="-linear %s",
-        position=1,
         desc=(
             "Specify a linear transform to apply, in the form of a 3x4 or 4x4 ascii file. "
             "Note the standard reverse convention is used, "
@@ -838,38 +836,32 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec):
     )
     replace_transform = traits.Bool(
         argstr="-replace",
-        position=1,
         desc="replace the current transform by that specified, rather than applying it to the current transform",
     )
     transformation_file = File(
         exists=True,
         argstr="-transform %s",
-        position=1,
         desc="The transform to apply, in the form of a 4x4 ascii file.",
     )
     template_image = File(
         exists=True,
         argstr="-template %s",
-        position=1,
         desc="Reslice the input image to match the specified template image.",
     )
     reference_image = File(
         exists=True,
         argstr="-reference %s",
-        position=1,
         desc="in case the transform supplied maps from the input image onto a reference image, use this option to specify the reference. Note that this implicitly sets the -replace option.",
     )
     flip_x = traits.Bool(
         argstr="-flipx",
-        position=1,
         desc="assume the transform is supplied assuming a coordinate system with the x-axis reversed relative to the MRtrix convention (i.e. x increases from right to left). This is required to handle transform matrices produced by FSL's FLIRT command. This is only used in conjunction with the -reference option.",
     )
     quiet = traits.Bool(
         argstr="-quiet",
-        position=1,
         desc="Do not display information messages or progress status.",
     )
-    debug = traits.Bool(argstr="-debug", position=1, desc="Display debugging messages.")
+    debug = traits.Bool(argstr="-debug", desc="Display debugging messages.")
 
 
 class MRTransformOutputSpec(TraitedSpec):

From 0d0d3ff1283d45cdf9d84e6de10a400078021537 Mon Sep 17 00:00:00 2001
From: manuegrx <47973414+manuegrx@users.noreply.github.com>
Date: Tue, 10 Oct 2023 10:21:20 +0200
Subject: [PATCH 02/26] add test create by check-before-commit

---
 nipype/interfaces/mrtrix3/tests/test_auto_MRTransform.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRTransform.py
index b50ee2c67f..e0337da2a9 100644
--- a/nipype/interfaces/mrtrix3/tests/test_auto_MRTransform.py
+++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRTransform.py
@@ -12,7 +12,6 @@ def test_MRTransform_inputs():
         ),
         debug=dict(
             argstr="-debug",
-            position=1,
         ),
         environ=dict(
             nohash=True,
@@ -20,7 +19,6 @@ def test_MRTransform_inputs():
         ),
         flip_x=dict(
             argstr="-flipx",
-            position=1,
         ),
         grad_file=dict(
             argstr="-grad %s",
@@ -45,12 +43,10 @@ def test_MRTransform_inputs():
         ),
         invert=dict(
             argstr="-inverse",
-            position=1,
         ),
         linear_transform=dict(
             argstr="-linear %s",
             extensions=None,
-            position=1,
         ),
         nthreads=dict(
             argstr="-nthreads %d",
@@ -71,26 +67,21 @@ def test_MRTransform_inputs():
         ),
         quiet=dict(
             argstr="-quiet",
-            position=1,
         ),
         reference_image=dict(
             argstr="-reference %s",
             extensions=None,
-            position=1,
         ),
         replace_transform=dict(
             argstr="-replace",
-            position=1,
         ),
         template_image=dict(
             argstr="-template %s",
             extensions=None,
-            position=1,
         ),
         transformation_file=dict(
             argstr="-transform %s",
             extensions=None,
-            position=1,
         ),
     )
     inputs = MRTransform.input_spec()

From b066807402ee07d908ce4f1b24ca69fef6b91809 Mon Sep 17 00:00:00 2001
From: Hans Johnson <hans.j.johnson@gmail.com>
Date: Wed, 26 Oct 2022 17:58:51 -0500
Subject: [PATCH 03/26] BUG: Reading serialized event requires conversion of
 dates

This patch attempts to convert string date representations
back to datetime.date objects so that compuations
can be done on them.
---
 nipype/utils/draw_gantt_chart.py | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py
index debce75970..6190e12fdf 100644
--- a/nipype/utils/draw_gantt_chart.py
+++ b/nipype/utils/draw_gantt_chart.py
@@ -103,8 +103,26 @@ def log_to_dict(logfile):
 
     nodes_list = [json.loads(l) for l in lines]
 
+    def _convert_string_to_datetime(datestring):
+        try:
+            datetime_object: datetime.datetime = datetime.datetime.strptime(
+                datestring, "%Y-%m-%dT%H:%M:%S.%f"
+            )
+            return datetime_object
+        except Exception as _:
+            pass
+        return datestring
+
+    date_object_node_list: list = list()
+    for n in nodes_list:
+        if "start" in n.keys():
+            n["start"] = _convert_string_to_datetime(n["start"])
+        if "finish" in n.keys():
+            n["finish"] = _convert_string_to_datetime(n["finish"])
+        date_object_node_list.append(n)
+
     # Return list of nodes
-    return nodes_list
+    return date_object_node_list
 
 
 def calculate_resource_timeseries(events, resource):
@@ -514,7 +532,11 @@ def generate_gantt_chart(
     # Create the header of the report with useful information
     start_node = nodes_list[0]
     last_node = nodes_list[-1]
-    duration = (last_node["finish"] - start_node["start"]).total_seconds()
+    duration: float = 0.0
+    if isinstance(start_node["start"], datetime.date) and isinstance(
+        last_node["finish"], datetime.date
+    ):
+        duration = (last_node["finish"] - start_node["start"]).total_seconds()
 
     # Get events based dictionary of node run stats
     events = create_event_dict(start_node["start"], nodes_list)

From 50be1a4acd53ee56bbeef93d038b497a62db334a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 5 Dec 2023 10:37:57 -0500
Subject: [PATCH 04/26] Add GenericLabel to ANTS ApplyTransforms.

---
 nipype/interfaces/ants/resampling.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nipype/interfaces/ants/resampling.py b/nipype/interfaces/ants/resampling.py
index 82a9e7a214..1b3e172756 100644
--- a/nipype/interfaces/ants/resampling.py
+++ b/nipype/interfaces/ants/resampling.py
@@ -349,6 +349,7 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
         "MultiLabel",
         "Gaussian",
         "BSpline",
+        "GenericLabel",
         argstr="%s",
         usedefault=True,
     )
@@ -497,6 +498,7 @@ def _format_arg(self, opt, spec, val):
                 "BSpline",
                 "MultiLabel",
                 "Gaussian",
+                "GenericLabel",
             ] and isdefined(self.inputs.interpolation_parameters):
                 return "--interpolation {}[ {} ]".format(
                     self.inputs.interpolation,

From 0114009b7b946844515997bffef2ab5fad965b35 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 5 Dec 2023 15:51:49 -0500
Subject: [PATCH 05/26] Address @effigies' review.

---
 nipype/interfaces/ants/resampling.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nipype/interfaces/ants/resampling.py b/nipype/interfaces/ants/resampling.py
index 1b3e172756..3a6ba2c724 100644
--- a/nipype/interfaces/ants/resampling.py
+++ b/nipype/interfaces/ants/resampling.py
@@ -358,6 +358,7 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
         traits.Tuple(
             traits.Float(), traits.Float()  # Gaussian/MultiLabel (sigma, alpha)
         ),
+        traits.Tuple(traits.Str()),  # GenericLabel
     )
     transforms = InputMultiObject(
         traits.Either(File(exists=True), "identity"),

From 71e8795d6f81d21baac754e10bb42b50d044c465 Mon Sep 17 00:00:00 2001
From: Horea Christian <chr@chymera.eu>
Date: Mon, 22 Jan 2024 10:52:12 -0500
Subject: [PATCH 06/26] Adjusted variable names for clarity and codespell false
 positives

---
 nipype/pipeline/engine/utils.py | 40 ++++++++++++++++-----------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
index 36122561e4..d947735cb0 100644
--- a/nipype/pipeline/engine/utils.py
+++ b/nipype/pipeline/engine/utils.py
@@ -510,15 +510,15 @@ def _write_detailed_dot(graph, dotfilename):
     edges = []
     for n in nx.topological_sort(graph):
         nodename = n.itername
-        inports = []
+        in_ports = []
         for u, v, d in graph.in_edges(nbunch=n, data=True):
             for cd in d["connect"]:
                 if isinstance(cd[0], (str, bytes)):
                     outport = cd[0]
                 else:
                     outport = cd[0][0]
-                inport = cd[1]
-                ipstrip = "in%s" % _replacefunk(inport)
+                in_port = cd[1]
+                ipstrip = "in%s" % _replacefunk(in_port)
                 opstrip = "out%s" % _replacefunk(outport)
                 edges.append(
                     "%s:%s:e -> %s:%s:w;"
@@ -529,11 +529,11 @@ def _write_detailed_dot(graph, dotfilename):
                         ipstrip,
                     )
                 )
-                if inport not in inports:
-                    inports.append(inport)
+                if in_port not in in_ports:
+                    in_ports.append(in_port)
         inputstr = (
             ["{IN"]
-            + [f"|<in{_replacefunk(ip)}> {ip}" for ip in sorted(inports)]
+            + [f"|<in{_replacefunk(ip)}> {ip}" for ip in sorted(in_ports)]
             + ["}"]
         )
         outports = []
@@ -886,34 +886,34 @@ def _node_ports(graph, node):
     for _, v, d in graph.out_edges(node, data=True):
         for src, dest in d["connect"]:
             if isinstance(src, tuple):
-                srcport = src[0]
+                src_port = src[0]
             else:
-                srcport = src
-            if srcport not in portoutputs:
-                portoutputs[srcport] = []
-            portoutputs[srcport].append((v, dest, src))
+                src_port = src
+            if src_port not in portoutputs:
+                portoutputs[src_port] = []
+            portoutputs[src_port].append((v, dest, src))
     return (portinputs, portoutputs)
 
 
 def _propagate_root_output(graph, node, field, connections):
     """Propagates the given graph root node output port
     field connections to the out-edge destination nodes."""
-    for destnode, inport, src in connections:
+    for destnode, in_port, src in connections:
         value = getattr(node.inputs, field)
         if isinstance(src, tuple):
             value = evaluate_connect_function(src[1], src[2], value)
-        destnode.set_input(inport, value)
+        destnode.set_input(in_port, value)
 
 
 def _propagate_internal_output(graph, node, field, connections, portinputs):
     """Propagates the given graph internal node output port
     field connections to the out-edge source node and in-edge
     destination nodes."""
-    for destnode, inport, src in connections:
+    for destnode, in_port, src in connections:
         if field in portinputs:
-            srcnode, srcport = portinputs[field]
-            if isinstance(srcport, tuple) and isinstance(src, tuple):
-                src_func = srcport[1].split("\\n")[0]
+            srcnode, src_port = portinputs[field]
+            if isinstance(src_port, tuple) and isinstance(src, tuple):
+                src_func = src_port[1].split("\\n")[0]
                 dst_func = src[1].split("\\n")[0]
                 raise ValueError(
                     "Does not support two inline functions "
@@ -924,9 +924,9 @@ def _propagate_internal_output(graph, node, field, connections, portinputs):
 
             connect = graph.get_edge_data(srcnode, destnode, default={"connect": []})
             if isinstance(src, tuple):
-                connect["connect"].append(((srcport, src[1], src[2]), inport))
+                connect["connect"].append(((src_port, src[1], src[2]), in_port))
             else:
-                connect = {"connect": [(srcport, inport)]}
+                connect = {"connect": [(src_port, in_port)]}
             old_connect = graph.get_edge_data(
                 srcnode, destnode, default={"connect": []}
             )
@@ -936,7 +936,7 @@ def _propagate_internal_output(graph, node, field, connections, portinputs):
             value = getattr(node.inputs, field)
             if isinstance(src, tuple):
                 value = evaluate_connect_function(src[1], src[2], value)
-            destnode.set_input(inport, value)
+            destnode.set_input(in_port, value)
 
 
 def generate_expanded_graph(graph_in):

From 1ab6baedd14b3b7e451c155d4c8774192d3a710a Mon Sep 17 00:00:00 2001
From: Steffen Bollmann <stebo85@users.noreply.github.com>
Date: Mon, 12 Feb 2024 09:50:55 +1000
Subject: [PATCH 07/26] Fix wrong name, should be al_ea

---
 nipype/interfaces/afni/preprocess.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
index a60a9f4617..d4836cbd0c 100644
--- a/nipype/interfaces/afni/preprocess.py
+++ b/nipype/interfaces/afni/preprocess.py
@@ -180,7 +180,7 @@ class AlignEpiAnatPy(AFNIPythonCommand):
     >>> al_ea.cmdline # doctest: +ELLIPSIS
     'python2 ...align_epi_anat.py -anat structural.nii -epi_base 0 -epi_strip 3dAutomask -epi \
 functional.nii -save_skullstrip -suffix _al -tshift off -volreg off'
-    >>> res = allineate.run()  # doctest: +SKIP
+    >>> res = al_ea.run()  # doctest: +SKIP
 
     See Also
     --------

From 3afcd62bd9bfa3ee0b85c4db1c4eb0eacea577a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= <toomaserikanijarv@gmail.com>
Date: Tue, 20 Feb 2024 09:43:14 +0100
Subject: [PATCH 08/26] Update utils.py

- Added 'hsvs' option for 5ttgen function
---
 nipype/interfaces/mrtrix3/utils.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index 2ec7eba909..93196cc4e5 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -224,13 +224,14 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
         "fsl",
         "gif",
         "freesurfer",
+        "hsvs",
         argstr="%s",
         position=-3,
         mandatory=True,
         desc="tissue segmentation algorithm",
     )
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-2, desc="input image"
+        exists=False, argstr="%s", mandatory=True, position=-2, desc="input image"
     )
     out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")
 

From 367776d6f27c06d4a80df1ba9b309529fb8fcdb8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= <toomaserikanijarv@gmail.com>
Date: Tue, 20 Feb 2024 09:47:05 +0100
Subject: [PATCH 09/26] Update .zenodo.json

---
 .zenodo.json | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.zenodo.json b/.zenodo.json
index 4b8ae1f2a6..6e884e7594 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -911,6 +911,11 @@
       "name": "Wu, Jianxiao",
       "orcid": "0000-0002-4866-272X",
     },
+    {
+      "affiliation": "Lund University",
+      "name": "Anijärv, Toomas Erik",
+      "orcid": "0000-0002-3650-4230",
+    },
   ],
   "keywords": [
     "neuroimaging",

From c08e17b992c1fa069963f7b7910a7d66aea746ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= <toomaserikanijarv@gmail.com>
Date: Tue, 20 Feb 2024 13:51:11 +0100
Subject: [PATCH 10/26] Update utils.py

- Changed '-inverse' parameter location from 1 to 2 (otherwise cannot use together with -linear)
---
 nipype/interfaces/mrtrix3/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index 93196cc4e5..d0b474a76b 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -823,7 +823,7 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec):
     )
     invert = traits.Bool(
         argstr="-inverse",
-        position=1,
+        position=2,
         desc="Invert the specified transform before using it",
     )
     linear_transform = File(

From 445cd6d567157dec2b62906dd561384c7b8704a2 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 27 Feb 2024 14:26:06 -0500
Subject: [PATCH 11/26] Fix typos

---
 .codespellrc | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.codespellrc b/.codespellrc
index 4bc57b6662..1192e63c5b 100644
--- a/.codespellrc
+++ b/.codespellrc
@@ -9,4 +9,5 @@ skip = .git,*.pdf,*.svg,external
 # Reson - short journal name
 # ALS, FWE - neuroimaging specific abbrevs
 # Comision - foreign word used
-ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile
+# expad - AFNI flag
+ignore-words-list = te,inport,objekt,jist,nd,hel,inout,fith,whos,fot,ue,shs,smal,nam,filetest,suh,noo,reson,als,fwe,crasher,comision,afile,expad

From 457cf3c866667c54d8dc2c3c477d073388d0a47f Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 27 Feb 2024 14:27:50 -0500
Subject: [PATCH 12/26] Update pre-commit hooks

---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4c68f0d3f0..c1bda308da 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,17 +2,17 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.2.0
     hooks:
       - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
     - id: codespell

From f1cbc1c941f8d02659f8ef245aac0862efb80ccf Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 27 Feb 2024 14:28:18 -0500
Subject: [PATCH 13/26] STY: black 2024.2 [ignore-rev]

---
 nipype/algorithms/modelgen.py                   | 6 +++---
 nipype/algorithms/rapidart.py                   | 6 +++---
 nipype/caching/memory.py                        | 1 +
 nipype/interfaces/ants/legacy.py                | 1 -
 nipype/interfaces/ants/registration.py          | 1 +
 nipype/interfaces/ants/resampling.py            | 1 +
 nipype/interfaces/ants/segmentation.py          | 1 +
 nipype/interfaces/ants/utils.py                 | 1 +
 nipype/interfaces/base/core.py                  | 8 +++++---
 nipype/interfaces/c3.py                         | 1 +
 nipype/interfaces/cmtk/__init__.py              | 1 +
 nipype/interfaces/dcm2nii.py                    | 1 +
 nipype/interfaces/diffusion_toolkit/__init__.py | 1 +
 nipype/interfaces/dipy/__init__.py              | 1 +
 nipype/interfaces/dipy/reconstruction.py        | 1 +
 nipype/interfaces/dtitk/__init__.py             | 1 +
 nipype/interfaces/fsl/epi.py                    | 6 +++---
 nipype/interfaces/fsl/tests/test_preprocess.py  | 2 +-
 nipype/interfaces/mipav/__init__.py             | 1 +
 nipype/interfaces/mne/__init__.py               | 1 +
 nipype/interfaces/nipy/__init__.py              | 1 +
 nipype/interfaces/semtools/__init__.py          | 1 +
 nipype/interfaces/slicer/__init__.py            | 1 +
 nipype/interfaces/slicer/generate_classes.py    | 1 +
 nipype/pipeline/plugins/dagman.py               | 1 +
 nipype/pipeline/plugins/oar.py                  | 1 +
 nipype/pipeline/plugins/pbs.py                  | 1 +
 nipype/pipeline/plugins/pbsgraph.py             | 1 +
 nipype/pipeline/plugins/sge.py                  | 1 +
 nipype/pipeline/plugins/sgegraph.py             | 1 +
 nipype/pipeline/plugins/slurm.py                | 1 +
 nipype/pipeline/plugins/slurmgraph.py           | 1 +
 nipype/scripts/instance.py                      | 1 +
 nipype/scripts/utils.py                         | 1 -
 nipype/sphinxext/apidoc/__init__.py             | 1 +
 nipype/sphinxext/documenter.py                  | 1 +
 nipype/sphinxext/gh.py                          | 1 +
 nipype/utils/functions.py                       | 1 +
 nipype/utils/imagemanip.py                      | 1 +
 39 files changed, 47 insertions(+), 15 deletions(-)

diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py
index e2656a0478..8487ac0264 100644
--- a/nipype/algorithms/modelgen.py
+++ b/nipype/algorithms/modelgen.py
@@ -417,9 +417,9 @@ def _generate_standard_design(
                                 sessinfo[i]["cond"][cid]["pmod"][j]["poly"] = info.pmod[
                                     cid
                                 ].poly[j]
-                                sessinfo[i]["cond"][cid]["pmod"][j][
-                                    "param"
-                                ] = info.pmod[cid].param[j]
+                                sessinfo[i]["cond"][cid]["pmod"][j]["param"] = (
+                                    info.pmod[cid].param[j]
+                                )
 
             sessinfo[i]["regress"] = []
             if hasattr(info, "regressors") and info.regressors is not None:
diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py
index 6063c5325f..99abf55b84 100644
--- a/nipype/algorithms/rapidart.py
+++ b/nipype/algorithms/rapidart.py
@@ -584,9 +584,9 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
             if displacement is not None:
                 dmap = np.zeros((x, y, z, timepoints), dtype=np.float64)
                 for i in range(timepoints):
-                    dmap[
-                        voxel_coords[0], voxel_coords[1], voxel_coords[2], i
-                    ] = displacement[i, :]
+                    dmap[voxel_coords[0], voxel_coords[1], voxel_coords[2], i] = (
+                        displacement[i, :]
+                    )
                 dimg = Nifti1Image(dmap, affine)
                 dimg.to_filename(displacementfile)
         else:
diff --git a/nipype/caching/memory.py b/nipype/caching/memory.py
index c941b48b41..a1d45ffff2 100644
--- a/nipype/caching/memory.py
+++ b/nipype/caching/memory.py
@@ -2,6 +2,7 @@
 Using nipype with persistence and lazy recomputation but without explicit
 name-steps pipeline: getting back scope in command-line based programming.
 """
+
 import os
 import hashlib
 import pickle
diff --git a/nipype/interfaces/ants/legacy.py b/nipype/interfaces/ants/legacy.py
index 447e8afa83..373ca4982a 100644
--- a/nipype/interfaces/ants/legacy.py
+++ b/nipype/interfaces/ants/legacy.py
@@ -4,7 +4,6 @@
 are preserved for backwards compatibility.
 """
 
-
 import os
 from glob import glob
 
diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py
index 6312d8aa30..13fe55739c 100644
--- a/nipype/interfaces/ants/registration.py
+++ b/nipype/interfaces/ants/registration.py
@@ -1,6 +1,7 @@
 """The ants module provides basic functions for interfacing with ants
    functions.
 """
+
 import os
 
 from ...utils.filemanip import ensure_list
diff --git a/nipype/interfaces/ants/resampling.py b/nipype/interfaces/ants/resampling.py
index 3a6ba2c724..c91b90238c 100644
--- a/nipype/interfaces/ants/resampling.py
+++ b/nipype/interfaces/ants/resampling.py
@@ -1,5 +1,6 @@
 """ANTS Apply Transforms interface
 """
+
 import os
 
 from .base import ANTSCommand, ANTSCommandInputSpec
diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py
index 11119cbde7..76c0ef152d 100644
--- a/nipype/interfaces/ants/segmentation.py
+++ b/nipype/interfaces/ants/segmentation.py
@@ -1,4 +1,5 @@
 """Wrappers for segmentation utilities within ANTs."""
+
 import os
 from glob import glob
 from ...external.due import BibTeX
diff --git a/nipype/interfaces/ants/utils.py b/nipype/interfaces/ants/utils.py
index a2f57935f4..dd81aedd30 100644
--- a/nipype/interfaces/ants/utils.py
+++ b/nipype/interfaces/ants/utils.py
@@ -1,4 +1,5 @@
 """ANTs' utilities."""
+
 import os
 from warnings import warn
 from ..base import traits, isdefined, TraitedSpec, File, Str, InputMultiObject
diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
index 797b90e741..6f60a13063 100644
--- a/nipype/interfaces/base/core.py
+++ b/nipype/interfaces/base/core.py
@@ -380,9 +380,11 @@ def run(self, cwd=None, ignore_exception=None, **inputs):
         """
         rtc = RuntimeContext(
             resource_monitor=config.resource_monitor and self.resource_monitor,
-            ignore_exception=ignore_exception
-            if ignore_exception is not None
-            else self.ignore_exception,
+            ignore_exception=(
+                ignore_exception
+                if ignore_exception is not None
+                else self.ignore_exception
+            ),
         )
 
         with indirectory(cwd or os.getcwd()):
diff --git a/nipype/interfaces/c3.py b/nipype/interfaces/c3.py
index 534d652b86..3871120d2c 100644
--- a/nipype/interfaces/c3.py
+++ b/nipype/interfaces/c3.py
@@ -1,4 +1,5 @@
 """Convert3D is a command-line tool for converting 3D images between common file formats."""
+
 import os
 from glob import glob
 
diff --git a/nipype/interfaces/cmtk/__init__.py b/nipype/interfaces/cmtk/__init__.py
index 426130e1a5..d71ac76e2c 100644
--- a/nipype/interfaces/cmtk/__init__.py
+++ b/nipype/interfaces/cmtk/__init__.py
@@ -1,4 +1,5 @@
 """CMP implements a full processing pipeline for creating connectomes with dMRI data."""
+
 from .cmtk import ROIGen, CreateMatrix, CreateNodes
 from .nx import NetworkXMetrics, AverageNetworks
 from .parcellation import Parcellate
diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py
index e37887a99c..05ba2c2951 100644
--- a/nipype/interfaces/dcm2nii.py
+++ b/nipype/interfaces/dcm2nii.py
@@ -1,4 +1,5 @@
 """dcm2nii converts images from the proprietary scanner DICOM format to NIfTI."""
+
 import os
 import re
 from copy import deepcopy
diff --git a/nipype/interfaces/diffusion_toolkit/__init__.py b/nipype/interfaces/diffusion_toolkit/__init__.py
index ef8dce7e4e..89b3d059ef 100644
--- a/nipype/interfaces/diffusion_toolkit/__init__.py
+++ b/nipype/interfaces/diffusion_toolkit/__init__.py
@@ -1,4 +1,5 @@
 """Diffusion Toolkit performs data reconstruction and fiber tracking on diffusion MR images."""
+
 from .base import Info
 from .postproc import SplineFilter, TrackMerge
 from .dti import DTIRecon, DTITracker
diff --git a/nipype/interfaces/dipy/__init__.py b/nipype/interfaces/dipy/__init__.py
index d12c13844f..aa74ee46f8 100644
--- a/nipype/interfaces/dipy/__init__.py
+++ b/nipype/interfaces/dipy/__init__.py
@@ -1,4 +1,5 @@
 """DIPY is a computational neuroimaging tool for diffusion MRI."""
+
 from .tracks import StreamlineTractography, TrackDensityMap
 from .tensors import TensorMode, DTI
 from .preprocess import Resample, Denoise
diff --git a/nipype/interfaces/dipy/reconstruction.py b/nipype/interfaces/dipy/reconstruction.py
index 7d39ab89d5..f242a76e29 100644
--- a/nipype/interfaces/dipy/reconstruction.py
+++ b/nipype/interfaces/dipy/reconstruction.py
@@ -2,6 +2,7 @@
 Interfaces to the reconstruction algorithms in dipy
 
 """
+
 import os.path as op
 
 import numpy as np
diff --git a/nipype/interfaces/dtitk/__init__.py b/nipype/interfaces/dtitk/__init__.py
index d1420c3afb..4210c1dd5d 100644
--- a/nipype/interfaces/dtitk/__init__.py
+++ b/nipype/interfaces/dtitk/__init__.py
@@ -5,6 +5,7 @@
 <http://dti-tk.sourceforge.net/pmwiki/pmwiki.php>`_ command line tools.
 
 """
+
 from .registration import (
     Rigid,
     Affine,
diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py
index 5b4f577e0a..09daacb17f 100644
--- a/nipype/interfaces/fsl/epi.py
+++ b/nipype/interfaces/fsl/epi.py
@@ -1059,9 +1059,9 @@ def _list_outputs(self):
         if os.path.exists(out_shell_alignment_parameters):
             outputs["out_shell_alignment_parameters"] = out_shell_alignment_parameters
         if os.path.exists(out_shell_pe_translation_parameters):
-            outputs[
-                "out_shell_pe_translation_parameters"
-            ] = out_shell_pe_translation_parameters
+            outputs["out_shell_pe_translation_parameters"] = (
+                out_shell_pe_translation_parameters
+            )
         if os.path.exists(out_outlier_map):
             outputs["out_outlier_map"] = out_outlier_map
         if os.path.exists(out_outlier_n_stdev_map):
diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py
index 72f663394f..e32e5c574f 100644
--- a/nipype/interfaces/fsl/tests/test_preprocess.py
+++ b/nipype/interfaces/fsl/tests/test_preprocess.py
@@ -70,7 +70,7 @@ def func():
         "center": ("-c 54 75 80", [54, 75, 80]),
         "threshold": ("-t", True),
         "mesh": ("-e", True),
-        "surfaces": ("-A", True)
+        "surfaces": ("-A", True),
         # 'verbose': ('-v', True),
         # 'flags': ('--i-made-this-up', '--i-made-this-up'),
     }
diff --git a/nipype/interfaces/mipav/__init__.py b/nipype/interfaces/mipav/__init__.py
index 51dd200dce..9cde4c0bcd 100644
--- a/nipype/interfaces/mipav/__init__.py
+++ b/nipype/interfaces/mipav/__init__.py
@@ -1,4 +1,5 @@
 """MIPAV enables quantitative analysis and visualization of multimodal medical images."""
+
 from .developer import (
     JistLaminarVolumetricLayering,
     JistBrainMgdmSegmentation,
diff --git a/nipype/interfaces/mne/__init__.py b/nipype/interfaces/mne/__init__.py
index 4a4750e8a4..7eba176251 100644
--- a/nipype/interfaces/mne/__init__.py
+++ b/nipype/interfaces/mne/__init__.py
@@ -1,2 +1,3 @@
 """MNE is a software for exploring, visualizing, and analyzing human neurophysiological data."""
+
 from .base import WatershedBEM
diff --git a/nipype/interfaces/nipy/__init__.py b/nipype/interfaces/nipy/__init__.py
index c7fee0b8d8..ad8b66d887 100644
--- a/nipype/interfaces/nipy/__init__.py
+++ b/nipype/interfaces/nipy/__init__.py
@@ -1,4 +1,5 @@
 """NIPY is a python project for analysis of structural and functional neuroimaging data."""
+
 from .model import FitGLM, EstimateContrast
 from .preprocess import ComputeMask, SpaceTimeRealigner
 from .utils import Similarity
diff --git a/nipype/interfaces/semtools/__init__.py b/nipype/interfaces/semtools/__init__.py
index ef43a28900..317273cfd8 100644
--- a/nipype/interfaces/semtools/__init__.py
+++ b/nipype/interfaces/semtools/__init__.py
@@ -1,4 +1,5 @@
 """SEM Tools are useful tools for Structural Equation Modeling."""
+
 from .diffusion import *
 from .featurecreator import GenerateCsfClippedFromClassifiedImage
 from .segmentation import *
diff --git a/nipype/interfaces/slicer/__init__.py b/nipype/interfaces/slicer/__init__.py
index d874ab88c4..ca191b99df 100644
--- a/nipype/interfaces/slicer/__init__.py
+++ b/nipype/interfaces/slicer/__init__.py
@@ -4,6 +4,7 @@
 For an EXPERIMENTAL implementation of an interface for the ``3dSlicer`` full framework,
 please check `"dynamic" Slicer <nipype.interfaces.dynamic_slicer.html>`__.
 """
+
 from .diffusion import *
 from .segmentation import *
 from .filtering import *
diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py
index 83f76c45b2..7c0c53bac6 100644
--- a/nipype/interfaces/slicer/generate_classes.py
+++ b/nipype/interfaces/slicer/generate_classes.py
@@ -2,6 +2,7 @@
 modules are selected from the hardcoded list below and generated code is placed
 in the cli_modules.py file (and imported in __init__.py). For this to work
 correctly you must have your CLI executables in $PATH"""
+
 import xml.dom.minidom
 import subprocess
 import os
diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py
index 42a73f0d8d..ad8e4ec733 100644
--- a/nipype/pipeline/plugins/dagman.py
+++ b/nipype/pipeline/plugins/dagman.py
@@ -1,5 +1,6 @@
 """Parallel workflow execution via Condor DAGMan
 """
+
 import os
 import sys
 import uuid
diff --git a/nipype/pipeline/plugins/oar.py b/nipype/pipeline/plugins/oar.py
index 0102d5b923..409d1746a5 100644
--- a/nipype/pipeline/plugins/oar.py
+++ b/nipype/pipeline/plugins/oar.py
@@ -1,5 +1,6 @@
 """Parallel workflow execution via OAR http://oar.imag.fr
 """
+
 import os
 import stat
 from time import sleep
diff --git a/nipype/pipeline/plugins/pbs.py b/nipype/pipeline/plugins/pbs.py
index 3106cc1122..e6e699efd0 100644
--- a/nipype/pipeline/plugins/pbs.py
+++ b/nipype/pipeline/plugins/pbs.py
@@ -1,5 +1,6 @@
 """Parallel workflow execution via PBS/Torque
 """
+
 import os
 from time import sleep
 
diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py
index 17c6db2964..4b245dedb7 100644
--- a/nipype/pipeline/plugins/pbsgraph.py
+++ b/nipype/pipeline/plugins/pbsgraph.py
@@ -1,5 +1,6 @@
 """Parallel workflow execution via PBS/Torque
 """
+
 import os
 import sys
 
diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py
index ac89f2dfea..8ddbb31791 100644
--- a/nipype/pipeline/plugins/sge.py
+++ b/nipype/pipeline/plugins/sge.py
@@ -1,5 +1,6 @@
 """Parallel workflow execution via SGE
 """
+
 import os
 import pwd
 import re
diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py
index 182619bd98..ad5fb78c44 100644
--- a/nipype/pipeline/plugins/sgegraph.py
+++ b/nipype/pipeline/plugins/sgegraph.py
@@ -1,5 +1,6 @@
 """Parallel workflow execution via SGE
 """
+
 import os
 import sys
 
diff --git a/nipype/pipeline/plugins/slurm.py b/nipype/pipeline/plugins/slurm.py
index 79fe28ee3d..cd37339695 100644
--- a/nipype/pipeline/plugins/slurm.py
+++ b/nipype/pipeline/plugins/slurm.py
@@ -5,6 +5,7 @@
 
 Parallel workflow execution with SLURM
 """
+
 import os
 import re
 from time import sleep
diff --git a/nipype/pipeline/plugins/slurmgraph.py b/nipype/pipeline/plugins/slurmgraph.py
index 901dc02a99..7d9ff0cc41 100644
--- a/nipype/pipeline/plugins/slurmgraph.py
+++ b/nipype/pipeline/plugins/slurmgraph.py
@@ -1,5 +1,6 @@
 """Parallel workflow execution via SLURM
 """
+
 import os
 import sys
 
diff --git a/nipype/scripts/instance.py b/nipype/scripts/instance.py
index 7bd2d7bf1b..f8712cf367 100644
--- a/nipype/scripts/instance.py
+++ b/nipype/scripts/instance.py
@@ -1,6 +1,7 @@
 """
 Import lib and class meta programming utilities.
 """
+
 import inspect
 import importlib
 
diff --git a/nipype/scripts/utils.py b/nipype/scripts/utils.py
index 00b0f8970e..77e7231bea 100644
--- a/nipype/scripts/utils.py
+++ b/nipype/scripts/utils.py
@@ -2,7 +2,6 @@
 Utilities for the CLI functions.
 """
 
-
 import re
 import click
 import json
diff --git a/nipype/sphinxext/apidoc/__init__.py b/nipype/sphinxext/apidoc/__init__.py
index 7392973536..151011bdfc 100644
--- a/nipype/sphinxext/apidoc/__init__.py
+++ b/nipype/sphinxext/apidoc/__init__.py
@@ -38,6 +38,7 @@ class Config(NapoleonConfig):
         (requires duecredit to be installed).
 
     """
+
     _config_values = {
         "nipype_skip_classes": (
             ["Tester", "InputSpec", "OutputSpec", "Numpy", "NipypeTester"],
diff --git a/nipype/sphinxext/documenter.py b/nipype/sphinxext/documenter.py
index 500c486927..eee0f626b9 100644
--- a/nipype/sphinxext/documenter.py
+++ b/nipype/sphinxext/documenter.py
@@ -1,4 +1,5 @@
 """sphinx autodoc ext."""
+
 from sphinx.locale import _
 from sphinx.ext import autodoc
 from nipype.interfaces.base import BaseInterface
diff --git a/nipype/sphinxext/gh.py b/nipype/sphinxext/gh.py
index 9339ddb48b..07a6513fb4 100644
--- a/nipype/sphinxext/gh.py
+++ b/nipype/sphinxext/gh.py
@@ -1,4 +1,5 @@
 """Build a file URL."""
+
 import os
 import inspect
 import subprocess
diff --git a/nipype/utils/functions.py b/nipype/utils/functions.py
index 1ef35b22b1..262f48665e 100644
--- a/nipype/utils/functions.py
+++ b/nipype/utils/functions.py
@@ -2,6 +2,7 @@
 Handles custom functions used in Function interface. Future imports
 are avoided to keep namespace as clear as possible.
 """
+
 import inspect
 from textwrap import dedent
 
diff --git a/nipype/utils/imagemanip.py b/nipype/utils/imagemanip.py
index 4fe022973b..15680dc6e4 100644
--- a/nipype/utils/imagemanip.py
+++ b/nipype/utils/imagemanip.py
@@ -1,4 +1,5 @@
 """Image manipulation utilities (mostly, NiBabel manipulations)."""
+
 import nibabel as nb
 
 

From d5cf21a075b26a5c9205fab66b7c5395973099fa Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 27 Feb 2024 14:30:13 -0500
Subject: [PATCH 14/26] chore: Update .git-blame-ignore-revs

---
 .git-blame-ignore-revs | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 8c1e119249..253c1c6919 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,3 +1,13 @@
+# Tue Feb 27 14:28:18 2024 -0500 - effigies@gmail.com - STY: black 2024.2 [ignore-rev]
+f1cbc1c941f8d02659f8ef245aac0862efb80ccf
+# Mon Sep 11 13:36:40 2023 +0200 - 37933899+servoz@users.noreply.github.com - run black for nipype/interfaces/spm/preprocess.py
+b9cac5e993143febb01ade42e56b41009427a4b6
+# Wed Jul 5 16:31:45 2023 -0400 - effigies@gmail.com - STY: Run black and fix typo
+34a4ac6eeff8d4924b40875c45df5d84a97da90b
+# Wed Jul 5 11:30:42 2023 -0400 - effigies@gmail.com - STY: black
+3b89ca85faf2428ecf7844de9c0db4aa7c329c93
+# Wed Jul 5 09:49:31 2023 -0400 - effigies@gmail.com - STY: black
+4a6a7d9d25d5d1e1f0eb55828dede58f8b9c9f80
 # Wed Apr 5 14:01:05 2023 -0400 - effigies@gmail.com - STY: black [ignore-rev]
 a9ce9b78a402ebacf7726ad6454bb75b1447f52f
 # Wed Sep 14 14:12:07 2022 -0400 - mathiasg@stanford.edu - STY: Black

From 056b48f23c896bed0fce1c571f33bb01922a1713 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 27 Feb 2024 14:35:34 -0500
Subject: [PATCH 15/26] chore: Update dependabot config to update all actions
 in one go

---
 .github/dependabot.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 3ab43cc7e7..61d6e0c09e 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -5,3 +5,7 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions-infrastructure:
+        patterns:
+          - "actions/*"

From 33a855f5eb8d521df26509d29abbb713c18da312 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 27 Feb 2024 19:36:54 +0000
Subject: [PATCH 16/26] Bump the actions-infrastructure group with 3 updates

Bumps the actions-infrastructure group with 3 updates: [actions/setup-python](https://github.com/actions/setup-python), [actions/upload-artifact](https://github.com/actions/upload-artifact) and [actions/download-artifact](https://github.com/actions/download-artifact).


Updates `actions/setup-python` from 4 to 5
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5)

Updates `actions/upload-artifact` from 3 to 4
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v3...v4)

Updates `actions/download-artifact` from 3 to 4
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/upload-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/download-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/contrib.yml |  4 ++--
 .github/workflows/tests.yml   | 14 +++++++-------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
index 2b35e7c831..67427e0e66 100644
--- a/.github/workflows/contrib.yml
+++ b/.github/workflows/contrib.yml
@@ -50,7 +50,7 @@ jobs:
           submodules: recursive
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -76,7 +76,7 @@ jobs:
           file: coverage.xml
         if: ${{ always() }}
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
           path: test-results.xml
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index c769cc9c71..ffd04e1878 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -40,14 +40,14 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - run: pip install --upgrade build twine
       - name: Build sdist and wheel
         run: python -m build
       - run: twine check dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/
@@ -59,11 +59,11 @@ jobs:
       matrix:
         package: ['wheel', 'sdist']
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3
       - name: Display Python version
@@ -124,7 +124,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -150,7 +150,7 @@ jobs:
           file: coverage.xml
         if: ${{ always() }}
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
           path: test-results.xml
@@ -162,7 +162,7 @@ jobs:
     needs: [stable, test-package]
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/

From caef07b7ab5a8f31398efa85265509bae158fccc Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Tue, 27 Feb 2024 16:37:17 -0500
Subject: [PATCH 17/26] Update .github/workflows/tests.yml

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ffd04e1878..899f2fc37b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -152,7 +152,7 @@ jobs:
       - name: Upload pytest test results
         uses: actions/upload-artifact@v4
         with:
-          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.deb-depends }}
           path: test-results.xml
         if: ${{ always() && matrix.check == 'test' }}
 

From 81d690c4386c1e964eefef9fa22a9ef1d28dbda7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 5 Feb 2024 04:30:48 +0000
Subject: [PATCH 18/26] Bump codecov/codecov-action from 3 to 4

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/contrib.yml | 2 +-
 .github/workflows/tests.yml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
index 2b35e7c831..f5d2f05001 100644
--- a/.github/workflows/contrib.yml
+++ b/.github/workflows/contrib.yml
@@ -71,7 +71,7 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: coverage.xml
         if: ${{ always() }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index c769cc9c71..fe0c56c64e 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -145,7 +145,7 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: coverage.xml
         if: ${{ always() }}

From 2f793c27e3016919a433e14c0638d5b0992e814c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Tue, 27 Feb 2024 16:40:28 -0500
Subject: [PATCH 19/26] Apply suggestions from code review

---
 .github/workflows/contrib.yml | 1 +
 .github/workflows/tests.yml   | 1 +
 2 files changed, 2 insertions(+)

diff --git a/.github/workflows/contrib.yml b/.github/workflows/contrib.yml
index f5d2f05001..97d9fd2ef2 100644
--- a/.github/workflows/contrib.yml
+++ b/.github/workflows/contrib.yml
@@ -74,6 +74,7 @@ jobs:
       - uses: codecov/codecov-action@v4
         with:
           file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
       - name: Upload pytest test results
         uses: actions/upload-artifact@v3
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index fe0c56c64e..93793281e5 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -148,6 +148,7 @@ jobs:
       - uses: codecov/codecov-action@v4
         with:
           file: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
       - name: Upload pytest test results
         uses: actions/upload-artifact@v3

From eda649755b4090ebaa959a771829fec1f9db3ba0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= <toomaserikanijarv@gmail.com>
Date: Wed, 28 Feb 2024 09:03:21 +0100
Subject: [PATCH 20/26] Fix generate5tt input

---
 nipype/interfaces/mrtrix3/utils.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index d0b474a76b..cb6b31ae91 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -11,6 +11,7 @@
     traits,
     TraitedSpec,
     File,
+    Directory,
     InputMultiPath,
     isdefined,
 )
@@ -230,8 +231,10 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
         mandatory=True,
         desc="tissue segmentation algorithm",
     )
-    in_file = File(
-        exists=False, argstr="%s", mandatory=True, position=-2, desc="input image"
+    in_file = traits.Either(
+        File(exists=True),
+        Directory(exists=True),
+        argstr="%s", mandatory=True, position=-2, desc="input image / directory"
     )
     out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")
 

From 7fc44fd9eb7eb80ef01c3253bb2cd72932389d48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= <toomaserikanijarv@gmail.com>
Date: Wed, 28 Feb 2024 09:07:45 +0100
Subject: [PATCH 21/26] Remove the -inverse parameter position change

---
 nipype/interfaces/mrtrix3/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index cb6b31ae91..cecbc6c855 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -826,7 +826,7 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec):
     )
     invert = traits.Bool(
         argstr="-inverse",
-        position=2,
+        position=1,
         desc="Invert the specified transform before using it",
     )
     linear_transform = File(

From 259210675c7db33927f2f70dbb0f215d8008f091 Mon Sep 17 00:00:00 2001
From: Martin Norgaard <martin.noergaard@nru.dk>
Date: Sun, 3 Mar 2024 20:09:36 +0100
Subject: [PATCH 22/26] ENH: add STC PVC to PETPVC interface

---
 nipype/interfaces/petpvc.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nipype/interfaces/petpvc.py b/nipype/interfaces/petpvc.py
index dbd1d805ed..ac388f6b51 100644
--- a/nipype/interfaces/petpvc.py
+++ b/nipype/interfaces/petpvc.py
@@ -37,6 +37,7 @@
     "RBV+VC",
     "RL",
     "VC",
+    "STC",
 ]
 
 
@@ -75,6 +76,7 @@ class PETPVCInputSpec(CommandLineInputSpec):
     * Muller Gartner -- ``MG``
     * Muller Gartner with Van-Cittert -- ``MG+VC``
     * Muller Gartner with Richardson-Lucy -- ``MG+RL``
+    * Single-target correction -- ``STC``
 
 """,
     )

From dcc249903b7957cffca61f6ff82761d615f273ce Mon Sep 17 00:00:00 2001
From: Zach Lindsey <zachery.lindsey@northwestern.edu>
Date: Wed, 13 Mar 2024 11:16:04 -0500
Subject: [PATCH 23/26] use csvreader for parsing csv files

---
 nipype/interfaces/utility/csv.py            | 15 ++++----
 nipype/interfaces/utility/tests/test_csv.py | 41 +++++++++++++++++++++
 2 files changed, 48 insertions(+), 8 deletions(-)

diff --git a/nipype/interfaces/utility/csv.py b/nipype/interfaces/utility/csv.py
index 3bfc46203d..da09e425fb 100644
--- a/nipype/interfaces/utility/csv.py
+++ b/nipype/interfaces/utility/csv.py
@@ -2,6 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """CSV Handling utilities
 """
+import csv
 from ..base import traits, TraitedSpec, DynamicTraitedSpec, File, BaseInterface
 from ..io import add_traits
 
@@ -13,6 +14,7 @@ class CSVReaderInputSpec(DynamicTraitedSpec, TraitedSpec):
     header = traits.Bool(
         False, usedefault=True, desc="True if the first line is a column header"
     )
+    delimiter = traits.String(",", usedefault=True, desc="Delimiter to use.")
 
 
 class CSVReader(BaseInterface):
@@ -52,14 +54,11 @@ def _append_entry(self, outputs, entry):
             outputs[key].append(value)
         return outputs
 
-    def _parse_line(self, line):
-        line = line.replace("\n", "")
-        entry = [x.strip() for x in line.split(",")]
-        return entry
-
     def _get_outfields(self):
         with open(self.inputs.in_file) as fid:
-            entry = self._parse_line(fid.readline())
+            reader = csv.reader(fid, delimiter=self.inputs.delimiter)
+
+            entry = next(reader)
             if self.inputs.header:
                 self._outfields = tuple(entry)
             else:
@@ -82,10 +81,10 @@ def _list_outputs(self):
         for key in self._outfields:
             outputs[key] = []  # initialize outfields
         with open(self.inputs.in_file) as fid:
-            for line in fid.readlines():
+            reader = csv.reader(fid, delimiter=self.inputs.delimiter)
+            for entry in reader:
                 if self.inputs.header and isHeader:  # skip header line
                     isHeader = False
                     continue
-                entry = self._parse_line(line)
                 outputs = self._append_entry(outputs, entry)
         return outputs
diff --git a/nipype/interfaces/utility/tests/test_csv.py b/nipype/interfaces/utility/tests/test_csv.py
index 923af9d837..3d4dcabe95 100644
--- a/nipype/interfaces/utility/tests/test_csv.py
+++ b/nipype/interfaces/utility/tests/test_csv.py
@@ -26,3 +26,44 @@ def test_csvReader(tmpdir):
                 assert out.outputs.column_0 == ["foo", "bar", "baz"]
                 assert out.outputs.column_1 == ["hello", "world", "goodbye"]
                 assert out.outputs.column_2 == ["300.1", "5", "0.3"]
+
+
+def test_csvReader_quoted(tmpdir):
+    header = "files,labels,erosion\n"
+    lines = ["foo,\"hello, world\",300.1\n"]
+
+    name = tmpdir.join("testfile.csv").strpath
+    with open(name, "w") as fid:
+        reader = utility.CSVReader()
+        fid.writelines(lines)
+        fid.flush()
+        reader.inputs.in_file = name
+        out = reader.run()
+
+        assert out.outputs.column_0 == ["foo"]
+        assert out.outputs.column_1 == ["hello, world"]
+        assert out.outputs.column_2 == ["300.1"]
+
+
+def test_csvReader_tabs(tmpdir):
+    header = "files\tlabels\terosion\n"
+    lines = ["foo\thello\t300.1\n", "bar\tworld\t5\n", "baz\tgoodbye\t0.3\n"]
+    for x in range(2):
+        name = tmpdir.join("testfile.csv").strpath
+        with open(name, "w") as fid:
+            reader = utility.CSVReader(delimiter="\t")
+            if x % 2 == 0:
+                fid.write(header)
+                reader.inputs.header = True
+            fid.writelines(lines)
+            fid.flush()
+            reader.inputs.in_file = name
+            out = reader.run()
+            if x % 2 == 0:
+                assert out.outputs.files == ["foo", "bar", "baz"]
+                assert out.outputs.labels == ["hello", "world", "goodbye"]
+                assert out.outputs.erosion == ["300.1", "5", "0.3"]
+            else:
+                assert out.outputs.column_0 == ["foo", "bar", "baz"]
+                assert out.outputs.column_1 == ["hello", "world", "goodbye"]
+                assert out.outputs.column_2 == ["300.1", "5", "0.3"]

From 5e84919fe1efd30524bf6c4a3b79d14d9be4a8de Mon Sep 17 00:00:00 2001
From: Zach Lindsey <zachery.lindsey@northwestern.edu>
Date: Wed, 13 Mar 2024 13:52:35 -0500
Subject: [PATCH 24/26] add csvreader autotest

---
 nipype/interfaces/utility/tests/test_auto_CSVReader.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nipype/interfaces/utility/tests/test_auto_CSVReader.py b/nipype/interfaces/utility/tests/test_auto_CSVReader.py
index be24c59eb4..a96a4d11bf 100644
--- a/nipype/interfaces/utility/tests/test_auto_CSVReader.py
+++ b/nipype/interfaces/utility/tests/test_auto_CSVReader.py
@@ -4,6 +4,9 @@
 
 def test_CSVReader_inputs():
     input_map = dict(
+        delimiter=dict(
+            usedefault=True,
+        ),
         header=dict(
             usedefault=True,
         ),

From f746c3408fe7e658bbc9cb0084c27540dc6d3a64 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sun, 17 Mar 2024 10:40:31 -0400
Subject: [PATCH 25/26] Update nipype/interfaces/utility/tests/test_csv.py

---
 nipype/interfaces/utility/tests/test_csv.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/utility/tests/test_csv.py b/nipype/interfaces/utility/tests/test_csv.py
index 3d4dcabe95..8a8f06e509 100644
--- a/nipype/interfaces/utility/tests/test_csv.py
+++ b/nipype/interfaces/utility/tests/test_csv.py
@@ -30,7 +30,7 @@ def test_csvReader(tmpdir):
 
 def test_csvReader_quoted(tmpdir):
     header = "files,labels,erosion\n"
-    lines = ["foo,\"hello, world\",300.1\n"]
+    lines = ['foo,"hello, world",300.1\n']
 
     name = tmpdir.join("testfile.csv").strpath
     with open(name, "w") as fid:

From f1a8909d233ed2a707b6ee8937504eea9ee7f154 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sun, 17 Mar 2024 10:44:57 -0400
Subject: [PATCH 26/26] STY: black

---
 nipype/interfaces/mrtrix3/utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index 3a35e7e534..ed6846cea7 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -234,7 +234,10 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
     in_file = traits.Either(
         File(exists=True),
         Directory(exists=True),
-        argstr="%s", mandatory=True, position=-2, desc="input image / directory"
+        argstr="%s",
+        mandatory=True,
+        position=-2,
+        desc="input image / directory",
     )
     out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")