Merge branch 'master' into dev_petprep

Author: effigies

.circleci/config.yml

@@ -133,8 +133,10 @@ jobs:
       - run:
           name: Setup git-annex and DataLad
           command: |
-            mamba install -y git-annex=*=alldep* unzip uv
+            mamba install -y unzip uv
+            uv tool install git-annex
             uv tool install --with=datalad-next --with=datalad-osf datalad
+            uv tool install --with=datalad-next datalad-osf
             git config --global user.name 'NiPreps Bot'
             git config --global user.email '[email protected]'
 

.github/workflows/codespell.yml

@@ -14,6 +14,6 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Codespell
         uses: codespell-project/actions-codespell@v2

.github/workflows/docs-build-pr.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
 

.github/workflows/docs-build-update.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ssh-key: "${{ secrets.NIPREPS_DEPLOY }}"
         fetch-depth: 0

.github/workflows/tox.yml

@@ -25,7 +25,7 @@ jobs:
     if: github.repository == 'nipreps/niworkflows'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - name: Set up Python 3
@@ -110,7 +110,7 @@ jobs:
       DEPENDS: ${{ matrix.dependencies }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: recursive
           fetch-depth: 0
@@ -156,7 +156,7 @@ jobs:
         check: ['style', 'spellcheck']
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Install the latest version of uv
         uses: astral-sh/setup-uv@v6
       - name: Install tox

.pre-commit-config.yaml

@@ -12,13 +12,10 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.12.2
     hooks:
       - name: ruff check --fix
-        id: ruff
+        id: ruff-check
         args: [ --fix ]
       - name: ruff format
         id: ruff-format
-      - name: fix implicit string concatenation
-        id: ruff
-        args: [ --select, ISC001, --fix ]

CHANGES.rst

@@ -1,3 +1,9 @@
+1.13.5 (June 19, 2025)
+======================
+Patch release in the 1.13.x series.
+
+* FIX: Allow optional/None filters to be overridden (#956)
+
 1.13.4 (June 05, 2025)
 ======================
 Patch release in the 1.13.x series.

niworkflows/data/nipreps.json

@@ -172,6 +172,7 @@
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_desc-{desc}]_{suffix<dseg>}{extension<.tsv|.json>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_desc-{desc}]_{suffix<morph>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}]_desc-{desc}_{suffix<mask>|mask}{extension<.label.gii|.json>|.label.gii}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|sbref|boldref|boldmap|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}[_desc-{desc}]_{suffix<xfm>|xfm}{extension<.txt|.h5>}",

niworkflows/utils/bids.py

@@ -242,6 +242,14 @@ def collect_data(
       ...
     ValueError: Conflicting entities for "session" found: madeup // retest
 
+    >>> bids_root, _ = collect_data(
+    ...     str(datadir / 'ds114'),
+    ...     '01',
+    ...     bids_validate=False,
+    ...     session_id=None,
+    ...     bids_filters={'t1w': {'session': 'retest'}})
+    >>> bids_root['t1w']  # doctest: +ELLIPSIS
+    ['.../ds114/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz']
     """
     if isinstance(bids_dir, BIDSLayout):
         layout = bids_dir
@@ -251,11 +259,12 @@ def collect_data(
     if not queries:
         queries = copy.deepcopy(DEFAULT_BIDS_QUERIES)
 
+    session_id = session_id or Query.OPTIONAL
     layout_get_kwargs = {
         'return_type': 'file',
         'subject': participant_label,
         'extension': ['.nii', '.nii.gz'],
-        'session': session_id or Query.OPTIONAL,
+        'session': session_id,
     }
 
     reserved_entities = [('subject', participant_label), ('session', session_id)]
@@ -264,6 +273,8 @@ def collect_data(
     for acq, entities in bids_filters.items():
         # BIDS filters will not be able to override subject / session entities
         for entity, param in reserved_entities:
+            if param == Query.OPTIONAL:
+                continue
             if entity in entities and listify(param) != listify(entities[entity]):
                 raise ValueError(
                     f'Conflicting entities for "{entity}" found: {entities[entity]} // {param}'

niworkflows/viz/plots.py

@@ -206,6 +206,8 @@ def plot_carpet(
     if detrend:
         from nilearn.signal import clean
 
+        if tr is not None:
+            tr = float(tr)
         data = clean(data.T, t_r=tr, filter=False).T
 
     # We want all subplots to have the same dynamic range
@@ -1090,6 +1092,7 @@ def get_surface_meshes(density, surface_type):
                 vmin=mn,
                 vmax=mx,
                 axes=ax,
+                colorbar=False,
                 **hemi_kwargs,
                 **kwargs,
             )