From 51da19b6ea2c686951273886ee83fb1d97aa36b9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 6 Feb 2024 14:10:32 -0500
Subject: [PATCH 01/20] Build(deps): Bump codecov/codecov-action from 3 to 4
 (#412)

* Build(deps): 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>

* CI: Pass token to codecov action

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
---
 .github/workflows/pythonpackage.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index d95b7c71f6..daf66fe141 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -109,8 +109,10 @@ jobs:
       run: python -m pip install "smriprep[tests]"
     - name: Run tests
       run: pytest -sv --doctest-modules --cov smriprep --pyargs smriprep
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
       name: Submit to CodeCov
+      with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   style:
     if: "!contains(github.event.head_commit.message, '[skip ci]')"

From 2355035d18d886cef5b6f0f4771e00c607d897a1 Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <mathiasg@stanford.edu>
Date: Wed, 28 Feb 2024 13:47:47 -0500
Subject: [PATCH 02/20] FIX: Re-add cohort identifier to template name (#416)

* FIX: Re-add cohort identifier to template name

* FIX: XFM io

* FIX: Query data with nipreps config

Also rename variables to play nice with pdb

* TST: Add test for derivatives ingestion

* PIN: niworkflows latest

* MAINT: Update ruff settings

* STY: ruff fixes

* TST: Ensure config is string

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 pyproject.toml                         |   8 +-
 smriprep/data/io_spec.json             |   8 +-
 smriprep/utils/bids.py                 |  37 ++++-----
 smriprep/utils/tests/__init__.py       |   5 ++
 smriprep/utils/tests/derivatives.yml   | 101 +++++++++++++++++++++++++
 smriprep/utils/tests/test_bids.py      |  30 ++++++++
 smriprep/workflows/fit/registration.py |  19 ++++-
 7 files changed, 183 insertions(+), 25 deletions(-)
 create mode 100644 smriprep/utils/tests/derivatives.yml
 create mode 100644 smriprep/utils/tests/test_bids.py

diff --git a/pyproject.toml b/pyproject.toml
index f57a362916..138234a55b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib >= 2.2.0",
     "nibabel >= 4.0.1",
     "nipype >= 1.7.0",
-    "niworkflows >= 1.8.0",
+    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
     "numpy",
     "packaging",
     "pybids >= 0.11.1",
@@ -138,6 +138,8 @@ source = [
 
 [tool.ruff]
 line-length = 99
+
+[tool.ruff.lint]
 extend-select = [
   "F",
   "E",
@@ -162,10 +164,10 @@ extend-select = [
   "Q",
 ]
 
-[tool.ruff.flake8-quotes]
+[tool.ruff.lint.flake8-quotes]
 inline-quotes = "single"
 
-[tool.ruff.extend-per-file-ignores]
+[tool.ruff.lint.extend-per-file-ignores]
 "*/test_*.py" = ["S101"]
 
 [tool.ruff.format]
diff --git a/smriprep/data/io_spec.json b/smriprep/data/io_spec.json
index 6b8fcd50fc..54edaf3ac1 100644
--- a/smriprep/data/io_spec.json
+++ b/smriprep/data/io_spec.json
@@ -50,8 +50,8 @@
       "forward": {
         "datatype": "anat",
         "extension": [
-          "h5",
-          "txt"
+          ".h5",
+          ".txt"
         ],
         "from": "T1w",
         "to": null,
@@ -61,8 +61,8 @@
       "reverse": {
         "datatype": "anat",
         "extension": [
-          "h5",
-          "txt"
+          ".h5",
+          ".txt"
         ],
         "from": null,
         "to": "T1w",
diff --git a/smriprep/utils/bids.py b/smriprep/utils/bids.py
index 123f8dd6c1..c213a0afc3 100644
--- a/smriprep/utils/bids.py
+++ b/smriprep/utils/bids.py
@@ -25,6 +25,7 @@
 from pathlib import Path
 
 from bids.layout import BIDSLayout
+from niworkflows.data import load as nwf_load
 
 from ..data import load_resource
 
@@ -39,36 +40,38 @@ def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patt
         if patterns is None:
             patterns = _patterns
 
-    layout = BIDSLayout(derivatives_dir, config=['bids', 'derivatives'], validate=False)
+    deriv_config = nwf_load('nipreps.json')
+    layout = BIDSLayout(derivatives_dir, config=deriv_config, validate=False)
 
     derivs_cache = {}
-    for k, q in spec['baseline'].items():
-        q['subject'] = subject_id
-        item = layout.get(return_type='filename', **q)
+    for key, qry in spec['baseline'].items():
+        qry['subject'] = subject_id
+        item = layout.get(return_type='filename', **qry)
         if not item:
             continue
 
-        derivs_cache['t1w_%s' % k] = item[0] if len(item) == 1 else item
+        derivs_cache[f't1w_{key}'] = item[0] if len(item) == 1 else item
 
     transforms = derivs_cache.setdefault('transforms', {})
-    for space in std_spaces:
-        for k, q in spec['transforms'].items():
-            q = q.copy()
-            q['subject'] = subject_id
-            q['from'] = q['from'] or space
-            q['to'] = q['to'] or space
-            item = layout.get(return_type='filename', **q)
+    for _space in std_spaces:
+        space = _space.replace(':cohort-', '+')
+        for key, qry in spec['transforms'].items():
+            qry = qry.copy()
+            qry['subject'] = subject_id
+            qry['from'] = qry['from'] or space
+            qry['to'] = qry['to'] or space
+            item = layout.get(return_type='filename', **qry)
             if not item:
                 continue
-            transforms.setdefault(space, {})[k] = item[0] if len(item) == 1 else item
+            transforms.setdefault(_space, {})[key] = item[0] if len(item) == 1 else item
 
-    for k, q in spec['surfaces'].items():
-        q['subject'] = subject_id
-        item = layout.get(return_type='filename', **q)
+    for key, qry in spec['surfaces'].items():
+        qry['subject'] = subject_id
+        item = layout.get(return_type='filename', **qry)
         if not item or len(item) != 2:
             continue
 
-        derivs_cache[k] = sorted(item)
+        derivs_cache[key] = sorted(item)
 
     return derivs_cache
 
diff --git a/smriprep/utils/tests/__init__.py b/smriprep/utils/tests/__init__.py
index e69de29bb2..84a88300dc 100644
--- a/smriprep/utils/tests/__init__.py
+++ b/smriprep/utils/tests/__init__.py
@@ -0,0 +1,5 @@
+from niworkflows.data import Loader
+
+load_data = Loader(__package__)
+
+DERIV_SKELETON = load_data('derivatives.yml')
diff --git a/smriprep/utils/tests/derivatives.yml b/smriprep/utils/tests/derivatives.yml
new file mode 100644
index 0000000000..97cda9e19c
--- /dev/null
+++ b/smriprep/utils/tests/derivatives.yml
@@ -0,0 +1,101 @@
+dataset_description:
+  Name: smriprep-outputs
+  BIDSVersion: 1.9.0
+  DatasetType: derivative
+'01':
+  anat:
+  - suffix: mask
+    desc: brain
+  - suffix: T1w
+    desc: preproc
+  - suffix: dseg
+  - suffix: probseg
+    label: CSF
+  - suffix: probseg
+    label: GM
+  - suffix: probseg
+    label: WM
+  - suffix: xfm
+    from: MNI152NLin2009cAsym
+    to: T1w
+    mode: image
+    extension: .h5
+  - suffix: xfm
+    from: T1w
+    to: MNI152NLin2009cAsym
+    mode: image
+    extension: .h5
+  - suffix: xfm
+    from: T1w
+    to: MNIPediatricAsym+3
+    mode: image
+    extension: .h5
+  - suffix: xfm
+    from: MNIPediatricAsym+3
+    to: T1w
+    mode: image
+    extension: .h5
+  - suffix: white
+    hemi: L
+    extension: .surf.gii
+  - suffix: white
+    hemi: R
+    extension: .surf.gii
+  - suffix: pial
+    hemi: L
+    extension: .surf.gii
+  - suffix: pial
+    hemi: R
+    extension: .surf.gii
+  - suffix: midthickness
+    hemi: L
+    extension: .surf.gii
+  - suffix: midthickness
+    hemi: R
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    space: fsLR
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    space: fsLR
+    desc: reg
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: L
+    space: fsLR
+    desc: msmsulc
+    extension: .surf.gii
+  - suffix: sphere
+    hemi: R
+    space: fsLR
+    desc: msmsulc
+    extension: .surf.gii
+  - suffix: thickness
+    hemi: L
+    extension: .shape.gii
+  - suffix: thickness
+    hemi: R
+    extension: .shape.gii
+  - suffix: sulc
+    hemi: L
+    extension: .shape.gii
+  - suffix: sulc
+    hemi: R
+    extension: .shape.gii
\ No newline at end of file
diff --git a/smriprep/utils/tests/test_bids.py b/smriprep/utils/tests/test_bids.py
new file mode 100644
index 0000000000..a8b094ea99
--- /dev/null
+++ b/smriprep/utils/tests/test_bids.py
@@ -0,0 +1,30 @@
+from niworkflows.utils.testing import generate_bids_skeleton
+
+from ..bids import collect_derivatives
+from . import DERIV_SKELETON
+
+
+def test_collect_derivatives(tmp_path):
+    deriv_dir = tmp_path / 'derivatives'
+    generate_bids_skeleton(deriv_dir, str(DERIV_SKELETON))
+    output_spaces = ['MNI152NLin2009cAsym', 'MNIPediatricAsym:cohort-3']
+    collected = collect_derivatives(deriv_dir, '01', output_spaces)
+    for suffix in ('preproc', 'mask', 'dseg'):
+        assert collected[f't1w_{suffix}']
+    assert len(collected['t1w_tpms']) == 3
+    xfms = collected['transforms']
+    for space in output_spaces:
+        assert xfms[space]['reverse']
+        assert xfms[space]['forward']
+    for surface in (
+        'white',
+        'pial',
+        'midthickness',
+        'sphere',
+        'thickness',
+        'sulc',
+        'sphere_reg',
+        'sphere_reg_fsLR',
+        'sphere_reg_msm',
+    ):
+        assert len(collected[surface]) == 2
diff --git a/smriprep/workflows/fit/registration.py b/smriprep/workflows/fit/registration.py
index 6e83212425..f9df9fb901 100644
--- a/smriprep/workflows/fit/registration.py
+++ b/smriprep/workflows/fit/registration.py
@@ -185,6 +185,12 @@ def init_register_template_wf(
         mem_gb=2,
     )
 
+    fmt_cohort = pe.Node(
+        niu.Function(function=_fmt_cohort, output_names=['template', 'spec']),
+        name='fmt_cohort',
+        run_without_submitting=True,
+    )
+
     # fmt:off
     workflow.connect([
         (inputnode, split_desc, [('template', 'template')]),
@@ -202,8 +208,12 @@ def init_register_template_wf(
         ]),
         (trunc_mov, registration, [
             ('output_image', 'moving_image')]),
-        (split_desc, outputnode, [
+        (split_desc, fmt_cohort, [
             ('name', 'template'),
+            ('spec', 'spec'),
+        ]),
+        (fmt_cohort, outputnode, [
+            ('template', 'template'),
             ('spec', 'template_spec'),
         ]),
         (registration, outputnode, [
@@ -225,3 +235,10 @@ def _make_outputnode(workflow, out_fields, joinsource):
         workflow.connect([(pout, out, [(f, f) for f in out_fields])])
         return pout
     return pe.Node(niu.IdentityInterface(fields=out_fields), name='outputnode')
+
+
+def _fmt_cohort(template, spec):
+    cohort = spec.pop('cohort', None)
+    if cohort is not None:
+        template = f'{template}:cohort-{cohort}'
+    return template, spec

From 8efea4b7d7b3c245bd5894b2f465a396525580c0 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 7 Mar 2024 14:02:44 -0500
Subject: [PATCH 03/20] CHORE: Update ruff, ignore certain rules

---
 .github/workflows/pythonpackage.yml | 2 +-
 .pre-commit-config.yaml             | 2 +-
 pyproject.toml                      | 5 +++++
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index daf66fe141..1d17c89d58 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -119,5 +119,5 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - run: pipx run ruff smriprep
+    - run: pipx run ruff check smriprep
     - run: pipx run ruff format --diff smriprep
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b6cf50e215..ee84b53cca 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
       - id: check-toml
       - id: check-json
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.2.0
     hooks:
       - id: ruff
       - id: ruff-format
diff --git a/pyproject.toml b/pyproject.toml
index 138234a55b..0bd878e582 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -163,6 +163,11 @@ extend-select = [
   "PT",
   "Q",
 ]
+extend-ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+  "S603",
+]
 
 [tool.ruff.lint.flake8-quotes]
 inline-quotes = "single"

From fb65496153313ca65e4f242f2ea0640e66cc378d Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <mathiasg@stanford.edu>
Date: Thu, 7 Mar 2024 14:34:43 -0500
Subject: [PATCH 04/20] Update .pre-commit-config.yaml

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ee84b53cca..c392fd2b85 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
       - id: check-toml
       - id: check-json
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.0
+    rev: v0.3.1
     hooks:
       - id: ruff
       - id: ruff-format

From 83a50d465145c6e8176c3f13d4673ed4e0bdb26f Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 7 Mar 2024 14:40:13 -0500
Subject: [PATCH 05/20] STY: ruff format smriprep [git-blame-ignore-rev]

---
 smriprep/__init__.py                   | 1 +
 smriprep/conf/__init__.py              | 1 +
 smriprep/interfaces/freesurfer.py      | 1 +
 smriprep/interfaces/gifti.py           | 1 +
 smriprep/interfaces/surf.py            | 1 +
 smriprep/interfaces/templateflow.py    | 1 +
 smriprep/utils/bids.py                 | 1 +
 smriprep/workflows/anatomical.py       | 1 +
 smriprep/workflows/base.py             | 1 +
 smriprep/workflows/fit/registration.py | 1 +
 smriprep/workflows/outputs.py          | 1 +
 smriprep/workflows/surfaces.py         | 1 +
 12 files changed, 12 insertions(+)

diff --git a/smriprep/__init__.py b/smriprep/__init__.py
index 13c2714ab2..8f41228dcb 100644
--- a/smriprep/__init__.py
+++ b/smriprep/__init__.py
@@ -8,6 +8,7 @@
 
 
 """
+
 from .__about__ import (
     __copyright__,
     __credits__,
diff --git a/smriprep/conf/__init__.py b/smriprep/conf/__init__.py
index 97cbd76598..39e82ec06a 100644
--- a/smriprep/conf/__init__.py
+++ b/smriprep/conf/__init__.py
@@ -1,4 +1,5 @@
 """sMRIPrep settings."""
+
 from templateflow.api import templates as _get_templates
 
 TF_TEMPLATES = tuple(_get_templates())
diff --git a/smriprep/interfaces/freesurfer.py b/smriprep/interfaces/freesurfer.py
index bd44550f9f..94cd2960fa 100644
--- a/smriprep/interfaces/freesurfer.py
+++ b/smriprep/interfaces/freesurfer.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Nipype's recon-all replacement."""
+
 import os
 
 from looseversion import LooseVersion
diff --git a/smriprep/interfaces/gifti.py b/smriprep/interfaces/gifti.py
index 08bc740bee..979902a191 100644
--- a/smriprep/interfaces/gifti.py
+++ b/smriprep/interfaces/gifti.py
@@ -1,4 +1,5 @@
 """Interfaces for manipulating GIFTI files."""
+
 import os
 
 import nibabel as nb
diff --git a/smriprep/interfaces/surf.py b/smriprep/interfaces/surf.py
index 107c679ca3..4022020b6a 100644
--- a/smriprep/interfaces/surf.py
+++ b/smriprep/interfaces/surf.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Handling surfaces."""
+
 import os
 from pathlib import Path
 
diff --git a/smriprep/interfaces/templateflow.py b/smriprep/interfaces/templateflow.py
index bb6374984c..e7199c8b94 100644
--- a/smriprep/interfaces/templateflow.py
+++ b/smriprep/interfaces/templateflow.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Interfaces to get templates from TemplateFlow."""
+
 import logging
 
 from nipype.interfaces.base import (
diff --git a/smriprep/utils/bids.py b/smriprep/utils/bids.py
index c213a0afc3..958cffa33b 100644
--- a/smriprep/utils/bids.py
+++ b/smriprep/utils/bids.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Utilities to handle BIDS inputs."""
+
 from json import loads
 from pathlib import Path
 
diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
index 305f3ed08e..e65620da47 100644
--- a/smriprep/workflows/anatomical.py
+++ b/smriprep/workflows/anatomical.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Anatomical reference preprocessing workflows."""
+
 import typing as ty
 
 from nipype import logging
diff --git a/smriprep/workflows/base.py b/smriprep/workflows/base.py
index a62ed135b1..5e1bda87e6 100644
--- a/smriprep/workflows/base.py
+++ b/smriprep/workflows/base.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """*sMRIPrep* base processing workflows."""
+
 import os
 import sys
 from copy import deepcopy
diff --git a/smriprep/workflows/fit/registration.py b/smriprep/workflows/fit/registration.py
index f9df9fb901..6365b3c7bc 100644
--- a/smriprep/workflows/fit/registration.py
+++ b/smriprep/workflows/fit/registration.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Spatial normalization workflows."""
+
 from collections import defaultdict
 
 from nipype.interfaces import ants
diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
index d7abe11f87..82f0f668c8 100644
--- a/smriprep/workflows/outputs.py
+++ b/smriprep/workflows/outputs.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Writing outputs."""
+
 import typing as ty
 
 from nipype.interfaces import utility as niu
diff --git a/smriprep/workflows/surfaces.py b/smriprep/workflows/surfaces.py
index 62ad2ea94b..b32c2e2862 100644
--- a/smriprep/workflows/surfaces.py
+++ b/smriprep/workflows/surfaces.py
@@ -27,6 +27,7 @@
 structural images.
 
 """
+
 import typing as ty
 
 from nipype.interfaces import freesurfer as fs

From 7378ee1562589cf42fc6aa754129911142cedaa4 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 7 Mar 2024 14:41:52 -0500
Subject: [PATCH 06/20] MNT: Update .git-blame-ignore-revs

---
 .git-blame-ignore-revs | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 663a141052..988964e066 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,3 +1,5 @@
+# 2024-03-07 - mathiasg@stanford.edu - STY: ruff format smriprep [git-blame-ignore-rev]
+83a50d465145c6e8176c3f13d4673ed4e0bdb26f
 # 2023-11-21 - effigies@gmail.com - STY: ruff --fix smriprep [git-blame-ignore-rev]
 3a586cf46cb1bb963b93d9546f20273194d15de5
 # 2023-11-20 - effigies@gmail.com - STY: ruff --fix smriprep [git-blame-ignore-rev]

From f30c2fd749baba31bf16bdd3ce2ab66c98126b16 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 1 Mar 2024 14:10:48 -0500
Subject: [PATCH 07/20] FIX: Ensure templates are pulled on workflow
 construction

---
 smriprep/utils/misc.py           | 27 +++++++++++++++++++++++++++
 smriprep/workflows/anatomical.py |  3 +++
 2 files changed, 30 insertions(+)

diff --git a/smriprep/utils/misc.py b/smriprep/utils/misc.py
index 3c473b49a2..60e6f726fd 100644
--- a/smriprep/utils/misc.py
+++ b/smriprep/utils/misc.py
@@ -21,6 +21,11 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Self-contained utilities to be used within Function nodes."""
+from pathlib import Path
+import typing as ty
+
+if ty.TYPE_CHECKING:
+    from niworkflows.utils.spaces import Reference
 
 
 def apply_lut(in_dseg, lut, newpath=None):
@@ -95,3 +100,25 @@ def fs_isRunning(subjects_dir, subject_id, mtime_tol=86400, logger=None):
     if logger:
         logger.warn(f'Removed "IsRunning*" files found under {subj_dir}')
     return subjects_dir
+
+
+def get_template_t1w(template: str, sloppy: bool = False) -> Path:
+    """Query templateflow for the T1w to ensure it is present on the filesystem."""
+    import templateflow.api as tf
+
+    spec = {}
+    _space = template.split(':', 1)
+    if len(_space) > 1:
+        spec['cohort'] = _space[1].replace('cohort-', '')
+    space = _space[0]
+
+    available_res = tf.TF_LAYOUT.get_resolutions(template=space)
+    if sloppy and 2 in available_res:
+        res = 2
+    elif 1 in available_res:
+        res = 1
+    else:
+        res = None
+    spec['resolution'] = res
+
+    return tf.get(space, desc=None, suffix='T1w', **spec)
diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
index e65620da47..3b1534c960 100644
--- a/smriprep/workflows/anatomical.py
+++ b/smriprep/workflows/anatomical.py
@@ -973,6 +973,9 @@ def init_anat_fit_wf(
     templates = []
     found_xfms = {}
     for template in spaces.get_spaces(nonstandard=False, dim=(3,)):
+        from ..utils.misc import get_template_t1w
+
+        get_template_t1w(template, sloppy)
         xfms = precomputed.get('transforms', {}).get(template, {})
         if set(xfms) != {'forward', 'reverse'}:
             templates.append(template)

From 718843992f8fb1cc558dbfd5c6effa441dc58db4 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 1 Mar 2024 16:31:50 -0500
Subject: [PATCH 08/20] FIX: Ensure sloppy resolution is used

---
 smriprep/workflows/anatomical.py |  3 ++-
 smriprep/workflows/outputs.py    | 16 ++++++++++++----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
index 3b1534c960..f8b121b38b 100644
--- a/smriprep/workflows/anatomical.py
+++ b/smriprep/workflows/anatomical.py
@@ -277,7 +277,7 @@ def init_anat_preproc_wf(
         omp_nthreads=omp_nthreads,
         skull_strip_fixed_seed=skull_strip_fixed_seed,
     )
-    template_iterator_wf = init_template_iterator_wf(spaces=spaces)
+    template_iterator_wf = init_template_iterator_wf(spaces=spaces, sloppy=sloppy)
     ds_std_volumes_wf = init_ds_anat_volumes_wf(
         bids_root=bids_root,
         output_dir=output_dir,
@@ -725,6 +725,7 @@ def init_anat_fit_wf(
         spaces=spaces,
         freesurfer=freesurfer,
         output_dir=output_dir,
+        sloppy=sloppy,
     )
     # fmt:off
     workflow.connect([
diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
index 82f0f668c8..0ac3fba8df 100644
--- a/smriprep/workflows/outputs.py
+++ b/smriprep/workflows/outputs.py
@@ -35,10 +35,13 @@
 from ..interfaces import DerivativesDataSink
 from ..interfaces.templateflow import TemplateFlowSelect
 
+if ty.TYPE_CHECKING:
+    from niworkflows.utils.spaces import SpatialReferences
+
 BIDS_TISSUE_ORDER = ('GM', 'WM', 'CSF')
 
 
-def init_anat_reports_wf(*, spaces, freesurfer, output_dir, name='anat_reports_wf'):
+def init_anat_reports_wf(*, spaces, freesurfer, output_dir, sloppy=False, name='anat_reports_wf'):
     """
     Set up a battery of datasinks to store reports in the right location.
 
@@ -131,7 +134,7 @@ def init_anat_reports_wf(*, spaces, freesurfer, output_dir, name='anat_reports_w
     # fmt:on
 
     if spaces._cached is not None and spaces.cached.references:
-        template_iterator_wf = init_template_iterator_wf(spaces=spaces)
+        template_iterator_wf = init_template_iterator_wf(spaces=spaces, sloppy=sloppy)
         t1w_std = pe.Node(
             ApplyTransforms(
                 dimension=3,
@@ -1112,7 +1115,12 @@ def init_anat_second_derivatives_wf(
     return workflow
 
 
-def init_template_iterator_wf(*, spaces, name='template_iterator_wf'):
+def init_template_iterator_wf(
+    *,
+    spaces: 'SpatialReferences',
+    sloppy: bool = False,
+    name='template_iterator_wf'
+):
     """Prepare the necessary components to resample an image to a template space
 
     This produces a workflow with an unjoined iterable named "spacesource".
@@ -1160,7 +1168,7 @@ def init_template_iterator_wf(*, spaces, name='template_iterator_wf'):
         run_without_submitting=True,
     )
     select_tpl = pe.Node(
-        TemplateFlowSelect(resolution=1), name='select_tpl', run_without_submitting=True
+        TemplateFlowSelect(resolution=2 if sloppy else 1), name='select_tpl', run_without_submitting=True
     )
 
     # fmt:off

From b7573676358de1af34ff758051cd74ebfc7d7cb5 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 6 Mar 2024 11:49:11 -0500
Subject: [PATCH 09/20] FIX: Determine resolution by sloppy parameter

---
 smriprep/workflows/outputs.py | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
index 0ac3fba8df..b99609a71f 100644
--- a/smriprep/workflows/outputs.py
+++ b/smriprep/workflows/outputs.py
@@ -1168,7 +1168,7 @@ def init_template_iterator_wf(
         run_without_submitting=True,
     )
     select_tpl = pe.Node(
-        TemplateFlowSelect(resolution=2 if sloppy else 1), name='select_tpl', run_without_submitting=True
+        TemplateFlowSelect(), name='select_tpl', run_without_submitting=True
     )
 
     # fmt:off
@@ -1185,7 +1185,7 @@ def init_template_iterator_wf(
         (spacesource, select_tpl, [
             ('space', 'template'),
             ('cohort', 'cohort'),
-            (('resolution', _no_native), 'resolution'),
+            (('resolution', _no_native, sloppy), 'resolution'),
         ]),
         (spacesource, outputnode, [
             ('space', 'space'),
@@ -1251,10 +1251,6 @@ def _pick_cohort(in_template):
     return [_pick_cohort(v) for v in in_template]
 
 
-def _fmt(in_template):
-    return in_template.replace(':', '_')
-
-
 def _empty_report(in_file=None):
     from pathlib import Path
 
@@ -1276,11 +1272,11 @@ def _is_native(value):
     return value == 'native'
 
 
-def _no_native(value):
+def _no_native(value, sloppy=False):
     try:
         return int(value)
     except (TypeError, ValueError):
-        return 1
+        return 2 if sloppy else 1
 
 
 def _drop_path(in_path):

From 97f4556ecb77cc8bd293c1bfbdbdfe52441effda Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 6 Mar 2024 13:50:53 -0500
Subject: [PATCH 10/20] RF: Strip out template fetching to separate function

---
 smriprep/interfaces/templateflow.py | 67 +++++++++++++++++------------
 smriprep/utils/misc.py              | 28 ------------
 2 files changed, 39 insertions(+), 56 deletions(-)

diff --git a/smriprep/interfaces/templateflow.py b/smriprep/interfaces/templateflow.py
index e7199c8b94..2a95893d48 100644
--- a/smriprep/interfaces/templateflow.py
+++ b/smriprep/interfaces/templateflow.py
@@ -108,34 +108,9 @@ def _run_interface(self, runtime):
         if isdefined(self.inputs.cohort):
             specs['cohort'] = self.inputs.cohort
 
-        name = self.inputs.template.strip(':').split(':', 1)
-        if len(name) > 1:
-            specs.update(
-                {
-                    k: v
-                    for modifier in name[1].split(':')
-                    for k, v in [tuple(modifier.split('-'))]
-                    if k not in specs
-                }
-            )
-
-        if specs['resolution'] and not isinstance(specs['resolution'], list):
-            specs['resolution'] = [specs['resolution']]
-
-        available_resolutions = tf.TF_LAYOUT.get_resolutions(template=name[0])
-        if specs['resolution'] and not set(specs['resolution']) & set(available_resolutions):
-            fallback_res = available_resolutions[0] if available_resolutions else None
-            LOGGER.warning(
-                f"Template {name[0]} does not have resolution(s): {specs['resolution']}."
-                f"Falling back to resolution: {fallback_res}."
-            )
-            specs['resolution'] = fallback_res
-
-        self._results['t1w_file'] = tf.get(name[0], desc=None, suffix='T1w', **specs)
-
-        self._results['brain_mask'] = tf.get(
-            name[0], desc='brain', suffix='mask', **specs
-        ) or tf.get(name[0], label='brain', suffix='mask', **specs)
+        files = fetch_template_files(self.inputs.template, specs)
+        self._results['t1w_file'] = files['t1w']
+        self._results['brain_mask'] = files['mask']
         return runtime
 
 
@@ -186,3 +161,39 @@ def _run_interface(self, runtime):
                 descsplit = desc.split('-')
                 self._results['spec'][descsplit[0]] = descsplit[1]
         return runtime
+
+
+def fetch_template_files(template: str, specs: dict | None = None) -> dict:
+    if specs is None:
+        specs = {}
+
+    name = template.strip(':').split(':', 1)
+    if len(name) > 1:
+        specs.update(
+            {
+                k: v
+                for modifier in name[1].split(':')
+                for k, v in [tuple(modifier.split('-'))]
+                if k not in specs
+            }
+        )
+
+    if specs['resolution'] and not isinstance(specs['resolution'], list):
+        specs['resolution'] = [specs['resolution']]
+
+    available_resolutions = tf.TF_LAYOUT.get_resolutions(template=name[0])
+    if specs['resolution'] and not set(specs['resolution']) & set(available_resolutions):
+        fallback_res = available_resolutions[0] if available_resolutions else None
+        LOGGER.warning(
+            f"Template {name[0]} does not have resolution(s): {specs['resolution']}."
+            f"Falling back to resolution: {fallback_res}."
+        )
+        specs['resolution'] = fallback_res
+
+    files = {}
+    files['t1w'] = tf.get(name[0], desc=None, suffix='T1w', **specs)
+    files['mask'] = (
+        tf.get(name[0], desc='brain', suffix='mask', **specs)
+        or tf.get(name[0], label='brain', suffix='mask', **specs)
+    )
+    return files
diff --git a/smriprep/utils/misc.py b/smriprep/utils/misc.py
index 60e6f726fd..2e399a7ad4 100644
--- a/smriprep/utils/misc.py
+++ b/smriprep/utils/misc.py
@@ -21,12 +21,6 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Self-contained utilities to be used within Function nodes."""
-from pathlib import Path
-import typing as ty
-
-if ty.TYPE_CHECKING:
-    from niworkflows.utils.spaces import Reference
-
 
 def apply_lut(in_dseg, lut, newpath=None):
     """Map the input discrete segmentation to a new label set (lookup table, LUT)."""
@@ -100,25 +94,3 @@ def fs_isRunning(subjects_dir, subject_id, mtime_tol=86400, logger=None):
     if logger:
         logger.warn(f'Removed "IsRunning*" files found under {subj_dir}')
     return subjects_dir
-
-
-def get_template_t1w(template: str, sloppy: bool = False) -> Path:
-    """Query templateflow for the T1w to ensure it is present on the filesystem."""
-    import templateflow.api as tf
-
-    spec = {}
-    _space = template.split(':', 1)
-    if len(_space) > 1:
-        spec['cohort'] = _space[1].replace('cohort-', '')
-    space = _space[0]
-
-    available_res = tf.TF_LAYOUT.get_resolutions(template=space)
-    if sloppy and 2 in available_res:
-        res = 2
-    elif 1 in available_res:
-        res = 1
-    else:
-        res = None
-    spec['resolution'] = res
-
-    return tf.get(space, desc=None, suffix='T1w', **spec)

From 5166979513efdc3a54a3255bd81abb62a36a1587 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Wed, 6 Mar 2024 14:25:54 -0500
Subject: [PATCH 11/20] FIX: Fetch templates during workflow construction

---
 smriprep/interfaces/templateflow.py | 17 ++++++++++++++---
 smriprep/workflows/anatomical.py    |  4 ++--
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/smriprep/interfaces/templateflow.py b/smriprep/interfaces/templateflow.py
index 2a95893d48..af38fa1b87 100644
--- a/smriprep/interfaces/templateflow.py
+++ b/smriprep/interfaces/templateflow.py
@@ -163,7 +163,11 @@ def _run_interface(self, runtime):
         return runtime
 
 
-def fetch_template_files(template: str, specs: dict | None = None) -> dict:
+def fetch_template_files(
+    template: str,
+    specs: dict | None = None,
+    sloppy: bool = False,
+) -> dict:
     if specs is None:
         specs = {}
 
@@ -178,11 +182,18 @@ def fetch_template_files(template: str, specs: dict | None = None) -> dict:
             }
         )
 
-    if specs['resolution'] and not isinstance(specs['resolution'], list):
+    if res := specs.pop('res', None):
+        if res != 'native':
+            specs['resolution'] = res
+
+    if not specs.get('resolution'):
+        specs['resolution'] = 2 if sloppy else 1
+
+    if specs.get('resolution') and not isinstance(specs['resolution'], list):
         specs['resolution'] = [specs['resolution']]
 
     available_resolutions = tf.TF_LAYOUT.get_resolutions(template=name[0])
-    if specs['resolution'] and not set(specs['resolution']) & set(available_resolutions):
+    if specs.get('resolution') and not set(specs['resolution']) & set(available_resolutions):
         fallback_res = available_resolutions[0] if available_resolutions else None
         LOGGER.warning(
             f"Template {name[0]} does not have resolution(s): {specs['resolution']}."
diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
index f8b121b38b..4135923aae 100644
--- a/smriprep/workflows/anatomical.py
+++ b/smriprep/workflows/anatomical.py
@@ -974,9 +974,9 @@ def init_anat_fit_wf(
     templates = []
     found_xfms = {}
     for template in spaces.get_spaces(nonstandard=False, dim=(3,)):
-        from ..utils.misc import get_template_t1w
+        from smriprep.interfaces.templateflow import fetch_template_files
 
-        get_template_t1w(template, sloppy)
+        fetch_template_files(template, specs=None, sloppy=sloppy)
         xfms = precomputed.get('transforms', {}).get(template, {})
         if set(xfms) != {'forward', 'reverse'}:
             templates.append(template)

From e351f9a4bdeca0744b396e6fef2770e37175cb46 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 7 Mar 2024 11:48:00 -0500
Subject: [PATCH 12/20] RF: Move template fetching to iterator workflow, adhere
 to style

---
 smriprep/interfaces/templateflow.py |  5 ++---
 smriprep/utils/misc.py              |  1 +
 smriprep/workflows/anatomical.py    |  3 ---
 smriprep/workflows/outputs.py       | 14 +++++++-------
 4 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/smriprep/interfaces/templateflow.py b/smriprep/interfaces/templateflow.py
index af38fa1b87..6a466d7d09 100644
--- a/smriprep/interfaces/templateflow.py
+++ b/smriprep/interfaces/templateflow.py
@@ -203,8 +203,7 @@ def fetch_template_files(
 
     files = {}
     files['t1w'] = tf.get(name[0], desc=None, suffix='T1w', **specs)
-    files['mask'] = (
-        tf.get(name[0], desc='brain', suffix='mask', **specs)
-        or tf.get(name[0], label='brain', suffix='mask', **specs)
+    files['mask'] = tf.get(name[0], desc='brain', suffix='mask', **specs) or tf.get(
+        name[0], label='brain', suffix='mask', **specs
     )
     return files
diff --git a/smriprep/utils/misc.py b/smriprep/utils/misc.py
index 2e399a7ad4..3c473b49a2 100644
--- a/smriprep/utils/misc.py
+++ b/smriprep/utils/misc.py
@@ -22,6 +22,7 @@
 #
 """Self-contained utilities to be used within Function nodes."""
 
+
 def apply_lut(in_dseg, lut, newpath=None):
     """Map the input discrete segmentation to a new label set (lookup table, LUT)."""
     import nibabel as nb
diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
index 4135923aae..4bdfd285c5 100644
--- a/smriprep/workflows/anatomical.py
+++ b/smriprep/workflows/anatomical.py
@@ -974,9 +974,6 @@ def init_anat_fit_wf(
     templates = []
     found_xfms = {}
     for template in spaces.get_spaces(nonstandard=False, dim=(3,)):
-        from smriprep.interfaces.templateflow import fetch_template_files
-
-        fetch_template_files(template, specs=None, sloppy=sloppy)
         xfms = precomputed.get('transforms', {}).get(template, {})
         if set(xfms) != {'forward', 'reverse'}:
             templates.append(template)
diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
index b99609a71f..9cf2f45ea3 100644
--- a/smriprep/workflows/outputs.py
+++ b/smriprep/workflows/outputs.py
@@ -1116,10 +1116,7 @@ def init_anat_second_derivatives_wf(
 
 
 def init_template_iterator_wf(
-    *,
-    spaces: 'SpatialReferences',
-    sloppy: bool = False,
-    name='template_iterator_wf'
+    *, spaces: 'SpatialReferences', sloppy: bool = False, name='template_iterator_wf'
 ):
     """Prepare the necessary components to resample an image to a template space
 
@@ -1130,6 +1127,11 @@ def init_template_iterator_wf(
 
     The fields in `outputnode` can be used as if they come from a single template.
     """
+    for template in spaces.get_spaces(nonstandard=False, dim=(3,)):
+        from smriprep.interfaces.templateflow import fetch_template_files
+
+        fetch_template_files(template, specs=None, sloppy=sloppy)
+
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(
@@ -1167,9 +1169,7 @@ def init_template_iterator_wf(
         name='select_xfm',
         run_without_submitting=True,
     )
-    select_tpl = pe.Node(
-        TemplateFlowSelect(), name='select_tpl', run_without_submitting=True
-    )
+    select_tpl = pe.Node(TemplateFlowSelect(), name='select_tpl', run_without_submitting=True)
 
     # fmt:off
     workflow.connect([

From 9f13a869266c84afa2f3925eded69a94408625c9 Mon Sep 17 00:00:00 2001
From: Mathias Goncalves <goncalves.mathias@gmail.com>
Date: Thu, 7 Mar 2024 14:45:29 -0500
Subject: [PATCH 13/20] Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 smriprep/workflows/outputs.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
index 9cf2f45ea3..dee84d17a0 100644
--- a/smriprep/workflows/outputs.py
+++ b/smriprep/workflows/outputs.py
@@ -33,7 +33,7 @@
 from niworkflows.interfaces.utility import KeySelect
 
 from ..interfaces import DerivativesDataSink
-from ..interfaces.templateflow import TemplateFlowSelect
+from ..interfaces.templateflow import TemplateFlowSelect, fetch_template_files
 
 if ty.TYPE_CHECKING:
     from niworkflows.utils.spaces import SpatialReferences
@@ -1128,8 +1128,6 @@ def init_template_iterator_wf(
     The fields in `outputnode` can be used as if they come from a single template.
     """
     for template in spaces.get_spaces(nonstandard=False, dim=(3,)):
-        from smriprep.interfaces.templateflow import fetch_template_files
-
         fetch_template_files(template, specs=None, sloppy=sloppy)
 
     workflow = pe.Workflow(name=name)

From 4cf06d3cd0b59e4c1fd9d7d8118d977debc6b5cb Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 8 Mar 2024 13:02:42 -0500
Subject: [PATCH 14/20] DOC: 0.14.0 changelog

---
 CHANGES.rst | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/CHANGES.rst b/CHANGES.rst
index 6d1fa38462..5a61cf35cd 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,3 +1,18 @@
+0.14.0 (March 08, 2024)
+=======================
+New feature release in the 0.14.x series.
+
+This release restores correct handling of cohort identifiers in templates.
+A feature release is warranted due to changes in the workflow structure.
+
+* FIX: Fetch templates during workflow construction (#418)
+* FIX: Re-add cohort identifier to template name (#416)
+* FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh) (#404)
+* FIX: Invert result of skull-strip check in auto mode (#402)
+* STY: Adopt ruff for linting and formatting (#397)
+* CHORE: Update ruff, ignore certain rules (#419)
+
+
 0.13.2 (December 08, 2023)
 ==========================
 Bug fix release in the 0.13.x series.

From 74a3745a15f87fe3f565a771e4c8a1625ce992ef Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 6 Mar 2024 14:52:51 -0500
Subject: [PATCH 15/20] Update pyproject requirements and env.yml

---
 env.yml        | 18 +++++++++---------
 pyproject.toml |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/env.yml b/env.yml
index 2e99487e37..6c4d96c74c 100644
--- a/env.yml
+++ b/env.yml
@@ -2,29 +2,29 @@ name: smriprep
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated April 2023
+# Update this ~yearly; last updated March 2024
 dependencies:
-  - python=3.10
+  - python=3.11
   # Needed for svgo and bids-validator; consider moving to deno
-  - nodejs=18
+  - nodejs=20
   # Intel Math Kernel Library for numpy
-  - mkl=2022.1
+  - mkl=2023.2
   - mkl-service=2.4
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
   - scipy=1.11
   - matplotlib=3.8
-  - pandas=2.1
+  - pandas=2.2
   - h5py=3.10
   # Dependencies compiled against numpy, best to stick with conda
   - scikit-image=0.22
-  - scikit-learn=1.3
+  - scikit-learn=1.4
   # Utilities
-  - graphviz=6.0
+  - graphviz=9.0
   - pandoc=3.1
   # Workflow dependencies: ANTs
-  - ants=2.5.0
-  # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
+  - ants=2.5
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
   - fsl-bet2=2111.4
   - fsl-flirt=2111.2
   - fsl-fast4=2111.3
diff --git a/pyproject.toml b/pyproject.toml
index 0bd878e582..b7b3e3a16b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ dependencies = [
     "matplotlib >= 2.2.0",
     "nibabel >= 4.0.1",
     "nipype >= 1.7.0",
-    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
+    "niworkflows >= 1.10.1",
     "numpy",
     "packaging",
     "pybids >= 0.11.1",

From 14ca542d240387842ac5e59599f86ea4a3e1340b Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 6 Mar 2024 14:53:12 -0500
Subject: [PATCH 16/20] chore(pin): echo "scipy<1.12" | uv pip compile
 --upgrade pyproject.toml -c - -p 3.11 -o requirements.txt

---
 requirements.txt | 93 +++++++++++++++++++-----------------------------
 1 file changed, 37 insertions(+), 56 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index fe4fbe0067..2d90f82d01 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,16 +1,12 @@
-#
-# This file is autogenerated by pip-compile with Python 3.11
-# by the following command:
-#
-#    pip-compile --strip-extras
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -c - -p 3.11 -o requirements.txt
 astor==0.8.1
     # via formulaic
-attrs==23.1.0
+attrs==23.2.0
     # via niworkflows
-bids-validator==1.13.1
+bids-validator==1.14.1
     # via pybids
-certifi==2023.11.17
+certifi==2024.2.2
     # via requests
 charset-normalizer==3.3.2
     # via requests
@@ -30,25 +26,24 @@ etelemetry==0.3.1
     # via nipype
 filelock==3.13.1
     # via nipype
-fonttools==4.44.3
+fonttools==4.49.0
     # via matplotlib
 formulaic==0.5.2
     # via pybids
-greenlet==3.0.1
+greenlet==3.0.3
     # via sqlalchemy
 h5py==3.10.0
     # via nitransforms
-idna==3.4
+idna==3.6
     # via requests
-imageio==2.32.0
+imageio==2.34.0
     # via scikit-image
 indexed-gzip==1.8.7
-    # via smriprep (pyproject.toml)
 interface-meta==1.3.0
     # via formulaic
 isodate==0.6.1
     # via rdflib
-jinja2==3.1.2
+jinja2==3.1.3
     # via niworkflows
 joblib==1.3.2
     # via
@@ -59,50 +54,43 @@ kiwisolver==1.4.5
 lazy-loader==0.3
     # via scikit-image
 lockfile==0.12.2
-    # via smriprep (pyproject.toml)
 looseversion==1.3.0
     # via
     #   nipype
     #   niworkflows
-    #   smriprep (pyproject.toml)
-lxml==4.9.3
+lxml==5.1.0
     # via
     #   nilearn
     #   prov
     #   svgutils
-markupsafe==2.1.3
+markupsafe==2.1.5
     # via jinja2
-matplotlib==3.8.2
+matplotlib==3.8.3
     # via
     #   niworkflows
     #   seaborn
-    #   smriprep (pyproject.toml)
 networkx==3.2.1
     # via
     #   nipype
     #   prov
     #   scikit-image
-nibabel==5.1.0
+nibabel==5.2.1
     # via
     #   nilearn
     #   nipype
     #   nitransforms
     #   niworkflows
     #   pybids
-    #   smriprep (pyproject.toml)
-nilearn==0.10.2
+nilearn==0.10.3
     # via niworkflows
 nipype==1.8.6
-    # via
-    #   niworkflows
-    #   smriprep (pyproject.toml)
+    # via niworkflows
 nitransforms==23.0.1
     # via niworkflows
-niworkflows==1.9.0
-    # via smriprep (pyproject.toml)
+niworkflows==1.10.1
 num2words==0.5.13
     # via pybids
-numpy==1.26.2
+numpy==1.26.4
     # via
     #   contourpy
     #   formulaic
@@ -120,7 +108,6 @@ numpy==1.26.2
     #   scikit-learn
     #   scipy
     #   seaborn
-    #   smriprep (pyproject.toml)
     #   tifffile
 packaging==23.2
     # via
@@ -131,45 +118,41 @@ packaging==23.2
     #   nipype
     #   niworkflows
     #   scikit-image
-    #   smriprep (pyproject.toml)
-pandas==2.1.3
+pandas==2.2.1
     # via
     #   formulaic
     #   nilearn
     #   niworkflows
     #   pybids
     #   seaborn
-pillow==10.0.1
+pillow==10.2.0
     # via
     #   imageio
     #   matplotlib
     #   scikit-image
 prov==2.0.0
     # via nipype
-pybids==0.16.3
+pybids==0.16.4
     # via
     #   niworkflows
-    #   smriprep (pyproject.toml)
     #   templateflow
-pydot==1.4.2
+pydot==2.0.0
     # via nipype
-pyparsing==3.1.1
+pyparsing==3.1.2
     # via
     #   matplotlib
     #   pydot
     #   rdflib
-python-dateutil==2.8.2
+python-dateutil==2.9.0.post0
     # via
     #   matplotlib
     #   nipype
     #   pandas
     #   prov
-pytz==2023.3.post1
+pytz==2024.1
     # via pandas
 pyyaml==6.0.1
-    # via
-    #   niworkflows
-    #   smriprep (pyproject.toml)
+    # via niworkflows
 rdflib==7.0.0
     # via
     #   nipype
@@ -181,7 +164,7 @@ requests==2.31.0
     #   templateflow
 scikit-image==0.22.0
     # via niworkflows
-scikit-learn==1.3.2
+scikit-learn==1.4.1.post1
     # via nilearn
 scipy==1.11.4
     # via
@@ -193,7 +176,7 @@ scipy==1.11.4
     #   pybids
     #   scikit-image
     #   scikit-learn
-seaborn==0.13.0
+seaborn==0.13.2
     # via niworkflows
 simplejson==3.19.2
     # via nipype
@@ -201,19 +184,17 @@ six==1.16.0
     # via
     #   isodate
     #   python-dateutil
-sqlalchemy==2.0.23
+sqlalchemy==2.0.28
     # via pybids
 svgutils==0.3.4
     # via niworkflows
-templateflow==23.1.0
-    # via
-    #   niworkflows
-    #   smriprep (pyproject.toml)
-threadpoolctl==3.2.0
+templateflow==24.0.0
+    # via niworkflows
+threadpoolctl==3.3.0
     # via scikit-learn
-tifffile==2023.9.26
+tifffile==2024.2.12
     # via scikit-image
-tqdm==4.66.1
+tqdm==4.66.2
     # via templateflow
 traits==6.3.2
     # via
@@ -221,13 +202,13 @@ traits==6.3.2
     #   niworkflows
 transforms3d==0.4.1
     # via niworkflows
-typing-extensions==4.8.0
+typing-extensions==4.10.0
     # via
     #   formulaic
     #   sqlalchemy
-tzdata==2023.3
+tzdata==2024.1
     # via pandas
-urllib3==2.1.0
+urllib3==2.2.1
     # via requests
 wrapt==1.16.0
     # via formulaic

From 201d28838e1975af7ecf3165402b028667461886 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 8 Mar 2024 13:47:41 -0500
Subject: [PATCH 17/20] chore(build): Sync Dockerfile to fmriprep

---
 Dockerfile | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 359528bec6..986380a701 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,7 +2,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2023 The NiPreps Developers
+# Copyright (c) The NiPreps Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,17 +23,17 @@
 # SOFTWARE.
 
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20230308
+ARG BASE_IMAGE=ubuntu:jammy-20240125
 
 #
-# sMRIPrep wheel
+# Build wheel
 #
 FROM python:slim AS src
 RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
-COPY . /src/smriprep
-RUN python -m build /src/smriprep
+COPY . /src
+RUN python -m build /src
 
 #
 # Download stages
@@ -41,6 +41,8 @@ RUN python -m build /src/smriprep
 
 # Utilities for downloading packages
 FROM ${BASE_IMAGE} as downloader
+# Bump the date to current to refresh curl/certificates/etc
+RUN echo "2023.07.20"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     binutils \
@@ -67,19 +69,30 @@ RUN mkdir /opt/workbench && \
 
 # Micromamba
 FROM downloader as micromamba
+
+# Install a C compiler to build extensions when needed.
+# traits<6.4 wheels are not available for Python 3.11+, but build easily.
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
 WORKDIR /
 # Bump the date to current to force update micromamba
-RUN echo "2023.04.05"
+RUN echo "2024.03.08"
 RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
 COPY env.yml /tmp/env.yml
 COPY requirements.txt /tmp/requirements.txt
+WORKDIR /tmp
 RUN micromamba create -y -f /tmp/env.yml && \
     micromamba clean -y -a
 
-ENV PATH="/opt/conda/envs/smriprep/bin:$PATH"
-RUN /opt/conda/envs/smriprep/bin/npm install -g svgo@^3.0 bids-validator@^1.13 && \
+# UV_USE_IO_URING for apparent race-condition (https://github.com/nodejs/node/issues/48444)
+# Check if this is still necessary when updating the base image.
+ENV PATH="/opt/conda/envs/smriprep/bin:$PATH" \
+    UV_USE_IO_URING=0
+RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
     rm -r ~/.npm
 
 #
@@ -179,7 +192,7 @@ ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
 # Installing SMRIPREP
-COPY --from=src /src/smriprep/dist/*.whl .
+COPY --from=src /src/dist/*.whl .
 RUN pip install --no-cache-dir $( ls *.whl )[telemetry,test]
 
 RUN find $HOME -type d -exec chmod go=u {} + && \

From 688df7d015588ec3fea2e6774e97bc34ec4a9e8c Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 8 Mar 2024 15:32:42 -0500
Subject: [PATCH 18/20] CI: Bump cimg, simplify pyenv, reset cache

---
 .circleci/config.yml | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ace45f1b1a..3854847095 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -4,14 +4,14 @@ _machine_defaults: &machine_defaults
     TZ: "/usr/share/zoneinfo/America/Los_Angeles"
     SCRATCH: "/scratch"
   machine:
-    image: ubuntu-2204:2023.04.2
+    image: default
     docker_layer_caching: true
   working_directory: /tmp/src/smriprep
   resource_class: large
 
 _python_defaults: &python_defaults
   docker:
-    - image: cimg/python:3.10.9
+    - image: cimg/python:3.12.2
       auth:
         username: $DOCKER_USER
         password: $DOCKER_PAT
@@ -115,8 +115,7 @@ jobs:
           name: Build Docker image
           no_output_timeout: 60m
           command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
+            pyenv local 3
             pip install hatch
             # Get version, update files.
             THISVERSION=$( hatch version )
@@ -139,8 +138,7 @@ jobs:
       - run:
           name: Check Docker image
           command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
+            pyenv local 3
             # Get version, update files.
             THISVERSION=$( hatch version )
             BUILT_VERSION=$( docker run --rm nipreps/smriprep:latest --version )
@@ -309,8 +307,7 @@ jobs:
       - run:
           name: Test smriprep-wrapper (Python 2)
           command: |
-            export PY2=$( pyenv versions | awk '/^\* 2/ { print $2 }' )
-            pyenv local $PY2
+            pyenv local 2.7
             echo -n "Python version: "
             python --version
             pip install --upgrade "pip<21"
@@ -322,8 +319,7 @@ jobs:
       - run:
           name: Test smriprep-wrapper (Python 3)
           command: |
-            export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' )
-            pyenv local $PY3
+            pyenv local 3
             echo -n "Python version: "
             python --version
             pip install --upgrade pip setuptools
@@ -440,10 +436,10 @@ jobs:
       - run: *pull_from_registry
       - restore_cache:
           keys:
-            - ds005-anat-v0-{{ .Branch }}-{{ epoch }}
-            - ds005-anat-v0-{{ .Branch }}
-            - ds005-anat-v0-master
-            - ds005-anat-v0-next
+            - ds005-anat-v1-{{ .Branch }}-{{ epoch }}
+            - ds005-anat-v1-{{ .Branch }}
+            - ds005-anat-v1-master
+            - ds005-anat-v1-next
       - restore_cache:
           keys:
             - testdata-v2-{{ .Branch }}-{{ epoch }}
@@ -500,7 +496,7 @@ jobs:
             rm -rf /tmp/ds005/work/reportlets
             rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
       - save_cache:
-          key: ds005-anat-v0-{{ .Branch }}-{{ epoch }}
+          key: ds005-anat-v1-{{ .Branch }}-{{ epoch }}
           paths:
             - /tmp/ds005/work
 

From 7d777a30b69354af66d063ac519d5b4b1d42931c Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 8 Mar 2024 16:07:29 -0500
Subject: [PATCH 19/20] CI: Sort expected outputs for consistency

---
 .circleci/config.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 3854847095..3c67a2d7ae 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -505,7 +505,8 @@ jobs:
           command: |
             mkdir -p /tmp/ds005/test
             find /tmp/ds005/derivatives -name "*" ! -path "*/figures*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
-            diff /tmp/src/smriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out
+            sort /tmp/src/smriprep/.circleci/ds005_outputs.txt > /tmp/ds005/test/expected.out
+            diff /tmp/ds005/test/{expected,outputs}.out
             exit $?
       - store_artifacts:
           path: /tmp/ds005/derivatives
@@ -636,7 +637,8 @@ jobs:
           command: |
             mkdir -p /tmp/ds054/test
             find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
-            diff /tmp/src/smriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out
+            sort /tmp/src/smriprep/.circleci/ds054_outputs.txt > /tmp/ds054/test/expected.out
+            diff /tmp/ds054/test/{expected,outputs}.out
             exit $?
       - run:
           name: Clean working directory

From 45c2e2fc088839979f18b83be630a6f9d515b416 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 11 Mar 2024 09:37:56 -0400
Subject: [PATCH 20/20] rel(0.14.0): update changes [skip ci]

---
 CHANGES.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGES.rst b/CHANGES.rst
index 5a61cf35cd..25155a24d1 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,4 +1,4 @@
-0.14.0 (March 08, 2024)
+0.14.0 (March 11, 2024)
 =======================
 New feature release in the 0.14.x series.