REL: 23.0.0 (#273)

* RM: Unused bold grouping

* MNT: Prepare changes for next release

* CI: Update pip first, avoid any prepended messages when checking version

* CI: Remove erroneous substitution

* DEP: Set nipreps to releases

Author: mgxd

.circleci/config.yml

@@ -518,7 +518,9 @@ jobs:
       - checkout
       - run:
           name: Update build tools
-          command: python -m pip install pip build twine hatch
+          command: |
+            python -m pip install -U pip
+            python -m pip install -U build twine hatch
       - run:
           name: Build nibabies
           command: python -m build
@@ -527,8 +529,7 @@ jobs:
       - run:
           name: Check sdist distribution
           command: |
-            THISVERSION=$( python -m hatch version )
-            THISVERSION=${THISVERSION%.d*}
+            THISVERSION=$( python -m hatch version | tail -n1 )
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
             python -m twine check dist/nibabies*.tar.gz
             virtualenv --python=python sdist
@@ -546,7 +547,6 @@ jobs:
           name: Check wheel distribution
           command: |
             THISVERSION=$( python -m hatch version )
-            THISVERSION=${THISVERSION%.d*}
             THISVERSION=${CIRCLE_TAG:-$THISVERSION}
             python -m twine check dist/nibabies*.whl
             virtualenv --python=python wheel
@@ -563,7 +563,6 @@ jobs:
           name: Build nibabies-wrapper
           command: |
             THISVERSION=$( python -m hatch version )
-            THISVERSION=${THISVERSION%.d*}
             python -m build wrapper/
       - store_artifacts:
           path: /tmp/src/nibabies/wrapper/dist
@@ -583,7 +582,6 @@ jobs:
           name: Build nibabies-wrapper
           command: |
             THISVERSION=$( python -m hatch version )
-            THISVERSION=${THISVERSION%.d*}
             python -m build wrapper/
       - run:
           name: Upload packages to PyPI

CHANGES.md

@@ -1,3 +1,21 @@
+23.0.0 (January 23, 2023)
+=========================
+New year, new *NiBabies* minor series!
+Some of the highlights of this release include:
+- New run-wise BOLD reference generation, prioritizing single-band references if available, unless avoided with the `--ignore sbrefs` flag.
+- New output: Preprocessed T2w in T1w space.
+
+A full list of changes can be found below.
+
+## Full Changelog
+  * ENH: Runwise bold reference generation (#268)
+  * ENH: Add preprocessed T2w volume to outputs (#271)
+  * MAINT: Drop versioneer for hatch backend, fully embrace pyproject.toml (#265)
+  * MAINT: Rotate CircleCI secrets and setup up org-level context (#266)
+  * CI: Bump convenience images, limit datalad (#267)
+  * FIX: Remove legacy CIFTI variant support (#264)
+
+
 22.2.0 (December 13, 2022)
 ==========================
 The final *NiBabies* minor series of 2022!

nibabies/utils/bids.py

@@ -127,111 +127,6 @@ def _unique(inlist):
     return {k: _unique(v) for k, v in entities.items()}
 
 
-def group_bolds_ref(*, layout, subject, sessions=None):
-    """
-    Extracts BOLD files from a BIDS dataset and combines them into buckets.
-    Files in a bucket share:
-    1) Session
-    2) Phase-encoding direction (PEdir)
-    3) Total readout time (TRT)
-
-    Any files with missing data for (2) or (3) are put in their own bucket.
-
-    Parameters
-    ----------
-    layout : pybids.layout.BIDSLayout
-        Initialized BIDSLayout
-    subject : str
-        The subject ID
-    sessions : None
-
-    Outputs
-    -------
-    combinations : list of tuples
-        Each tuple is composed of (session, PEdir, TRT)
-    files : list of lists
-        Files matching each combination.
-
-    Limitations
-    -----------
-    Single-band reference (sbref) are excluded.
-    """
-    import re
-    from contextlib import suppress
-    from itertools import product
-
-    from sdcflows.utils.epimanip import get_trt
-
-    base_entities = {
-        "subject": subject,
-        "extension": (".nii", ".nii.gz"),
-        "scope": "raw",  # Ensure derivatives are not captured
-    }
-    # dictionary containing unique Groupings and files
-    groupings = {}
-    # list of all BOLDS encountered
-    all_bolds = []
-
-    sessions = sessions if sessions else layout.get_sessions(subject=subject, scope="raw")
-
-    for ses, suffix in sorted(product(sessions or (None,), {"bold"})):
-        # bold files same session
-        bolds = layout.get(suffix=suffix, session=ses, **base_entities)
-        # some sessions may not have BOLD scans
-        if bolds is None:
-            continue
-
-        for i, bold in enumerate(bolds):
-            multiecho_id = None
-            # multi-echo should be grouped together
-            if 'echo' in bold.entities:
-                # create unique id by dropping "_echo-{i}"
-                multiecho_id = re.sub(r"_echo-\d+", "", bold.filename)
-
-            # session, pe, ro
-            meta = bold.get_metadata()
-            pe_dir = meta.get("PhaseEncodingDirection")
-
-            ro = None
-            with suppress(ValueError):
-                ro = get_trt(meta, bold.path)
-            if ro is not None:
-                meta.update({"TotalReadoutTime": ro})
-
-            grouping = BOLDGrouping(
-                session=ses,
-                pe_dir=pe_dir,
-                readout=ro,
-                multiecho_id=multiecho_id,
-            )
-
-            if any(v is None for v in (pe_dir, ro)):
-                # cannot be certain so treat as unique
-                grouping.add_file(bold.path)
-                groupings[f'unknown{i}'] = grouping
-            else:
-                try:
-                    grouping = groupings[grouping.name]
-                except KeyError:
-                    groupings[grouping.name] = grouping
-
-                grouping.add_file(bold.path)
-
-        all_bolds += bolds
-
-        if len(all_bolds) != sum([len(g.files) for _, g in groupings.items()]):
-            msg = f"""Error encountered when grouping BOLD runs.
-Combinations: {groupings}
-BOLD files: {bolds}
-
-Please file a bug-report with the nibabies developers at:
-https://github.com/nipreps/nibabies/issues/new/choose
-"""
-            raise RuntimeError(msg)
-
-    return groupings
-
-
 def validate_input_dir(exec_env, bids_dir, participant_label):
     # Ignore issues and warnings that should not influence NiBabies
     import subprocess

nibabies/workflows/base.py

@@ -51,7 +51,6 @@
 from .. import config
 from ..interfaces import DerivativesDataSink
 from ..interfaces.reports import AboutSummary, SubjectSummary
-from ..utils.bids import group_bolds_ref
 from .bold import init_func_preproc_wf
 
 

pyproject.toml

@@ -24,15 +24,15 @@ dependencies = [
     "nipype >= 1.8.1",
     "nitime",
     "nitransforms >= 21.0.0",
-    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
+    "niworkflows ~= 1.7.1",
     "numpy >= 1.21.0",
     "packaging",
     "pandas",
     "psutil >= 5.4",
     "pybids >= 0.15.0",
     "requests",
-    "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
+    "sdcflows ~= 2.2.2",
+    "smriprep ~= 0.10.0",
     "tedana ~= 0.0.12",
     "templateflow >= 0.6",
     "toml",